The first criteria of the principle of double-effect is that the principle of double-effect only applies when an act is not intrinsically immoral....Isn't it odd, then, that so many Catholics, including a number of well respected theologians in their non-magisterial texts, appeal to the principle of double-effect in order to demonstrate that a proposed act is not intrinsically immoral? This is exactly backward. The principle of double effect doesn't determine whether or not an act is intrinsically immoral: rather, the PDE applies only to acts which are not intrinsically immoral.
The principle of double effect does contribute an essential component to determining whether or not an act is intrinsically immoral, which, for instance, is why in ST 2-2.64.7, a locus classicus for the principle, Thomas Aquinas does exactly that. The reason is that the principle of double effect recognizes that there are effects intended and effects that are preter-intentional, beside the intention, and that this is relevant because changes in the intention change the act itself. Subtle changes may change it subtly, major changes will change it in a major way. Thus, if in a struggle you kill someone because you are trying to save your life, this is a different act entirely from, in the same struggle, trying to kill them because you want them dead. Thus drawing the line between intentional and preter-intentional effect is an important step in determining what the act is in the first place -- which certainly is a prerequisite if you are going to evaluate whether it is intrinsically immoral.
The confusion, I think, and I think it is a general one, is due to the fact that the principle of double effect in its actual applications usually involves two elements: the drawing of the line between intentional and preter-intentional effect, and the judgment that this line is also a line between permissible and impermissible acts. When we talk about double effect we sometimes mean the former and sometimes both the former and the latter. This latter judgment cannot be based on the distinction of effects alone. (Thus Aquinas, for instance, claims that it is permissible to kill someone as a preter-intentional effect of one's act, assuming that everything is done in a proportionate manner, because self-preservation is natural.) But to get to the point that you are properly understanding the act in question, you need to remove confusions about effects that lead to equivocation on the subject; and to do this you have to begin applying the principle of double effect. This is, of course, not a sufficient condition; but it certainly is a necessary one.
To put it in other terms: when you have determined that an act is intrinsically immoral, this means that it is immoral when you have taken into account every morally relevant feature of the act. Only then can you determine the actual object of this particular act. Thus it is trivially true that if an act is intrinsically immoral, applying the principle of double effect does not show it to be permissible, because recognizing it as intrinsically immoral involves already having taken into account the distinction of effects (otherwise we are being dangerously vague about which act we are talking about). Thus we have to have already applied the principle of double effect to judge that the particular act in question is intrinsically immoral. It is certainly true that the application of the distinction of effects does not on its own show that any act is permissible; what it does is identify one very important way in which people get confused about which act they are talking about -- and this confusion can in some cases be all the difference between an act that is permissible and an act that is impermissible. The permissibility (or impermissibility) has to be shown on other grounds. But in every case what we will be investigating is the permissibility or impermissibility of acts that the distinction of the double effect has distinguished. Given the distinction, there is a further step of saying that, in the case of an act in which a good effect is intended and a bad effect is preter-intentional, the bad effect's being preter-intentional is enough to make it permissible if:
(1) the particular way the good effect is intended is itself not intrinsically evil (we can, of course, intend good effects in intrinsically disordered ways, and many immoral actions involve intending good things in evil ways);
(2) the bad effect is permitted but not actively willed;
(3) the good effect is at least as natural an effect for that action as the bad effect;
(4) the good effect is substantially good in comparison with the bad effect.
There has historically been some controversy about how (4) is best determined, and about what exactly happens if conditions (2) or (3) are not met. Everyone agrees, though, that if all four conditions are met the act is permissible. In practice we tend sometimes to use 'principle of double effect' to refer to the distinction of effects (given that this can sometimes make apparently impermissible acts permissible) and sometime to use it to refer to the distinction plus a set of criteria of permissibility like the above. The former alone tells us nothing about permissibility, but it is necessary for determining whether any moral act is intrinsically evil or permissible. The latter does tell us whether an act is permissible; determining whether something is intrinsically evil or not is indeed a key element of it, but a great deal depends on whether you presume the new acts identified by the distinction to be intrinsically evil until proven permissible or permissible until proven impermissible.
We can sum it all up with an example. Murder is an intrinsically evil act. But to determine whether an act is murder requires first distinguishing intentional and preter-intentional effects, and recognizing that this distinction has important bearing on how the act is to be understood in the first place. So, faced with an act of killing, we consider what effects were intended and what effects were preter-intentional. Suppose someone tried to fend off an attacker, leading to the attacker's death. We then ask if the person who was attacked was concerned at the time with simply protecting his own life, and not bent on killing the attacker. Suppose it to be so. We then ask if the end of protecting one's own life is a good one to will. It is. We then ask if the person who was attacked used a reasonable amount of force in his defense (rather than, say, plunging a knife twenty times into the attacker's body). Suppose it to be so. This means that the means was proportionate to the end. We then ask if there was any general imprudence on the part of the person attacked. That is, we want to know whether the person attacked should have chosen some alternative course that would not have resulted in the attacker's death but would still have fully preserved the end of self-preservation. (It's possible, of course, that a person could genuinely intend self-preservation rather than murder, and in the act itself exercise restrain and a sense of proportion, but be certainly wrong for getting into the situation in the first place. A man in a duel to 'preserve his honor' may intend only self-preservation, and strictly restrain himself to proportionate means, but that doesn't of itself make the act of killing permissible.) This can be a tricky thing to evaluate; sometimes the imprudence will be minor, and simply will make the act less good than it usually would be, while often it will be major enough to make the good intention and proportionate means simply a component part of a larger immoral act. Suppose the person attacked were set upon suddenly and without warning, not having been negligent. Then there is nothing about the act that makes it wrong, however similar it may look to an act of outright murder under similar conditions.