In the interest of helping you cope with the "APT" hype, I thought I'd offer a few observations and ideas about things you can do that might actually help. After all, it's too easy to point and shout "hype" - the truth is that there is a problem, and system and network administrators who are concerned with security do have to worry about long-term embedded penetrations in their network.
There are two primary approaches to Intrusion Detection and they both work. But, they work against different threats, for different reasons. One is the 'classical' IDS approach: know what attack looks like, and look for the attack. That's what most of the signature-based IDS do, and they're good at it and therefore they are useful. The second is the 'analytical' approach (what Richard Bejtlich, in his excellent books, calls "network security monitoring"): know what your network and systems usually do, and begin an investigation if you see them suddenly start doing something new. As with everything, there are trade-offs. Some people would say that the first approach has a problem of "too many false positives" although, seriously, if your network is carrying such a large amount of apparently hostile traffic that your IDS is constantly ringing off the hook, I think you've already got a serious problem. The second approach has the problem that "start an investigation" may be outside the purview, skill set, or energy level of many system/network managers - especially now that the typical system/network admin is chief cook, busboy, and bottle-washer all rolled up in one.