Some truth to what you say, and some misconceptions.. All subs should be 'placed' and not just plunked down.. The method of putting the box in the sweet-spot and then crawling all over the floor does work.. The IB adds walls and ceilings to the mix.. So, just as Alex suggests using a ladder to check on surround placement, the same applies to the IB..
As for the crossover point being lower, not so.. A sub is a sub.. The type of installation does not change the laws of physics.. Box or IB, 8oHz is 80Hz.. Crossover settings are determinded by the speakers (mains,surrounds,center,subs) abilities, the room acoustics, audio source (movie, music), and your own personal tastes.. 80 hertz is common as most agree that is the point human hearing fails to be able to determine direction.. But again, that is subject to debate, your milage may vary..
Wave cancellation issues:
Sound waves start from a given source (mains,subs,etc) and proceed to bounce all over the freq'n room ! There are lots of excellent sites you can check out, so no need for me to go off on that one..
Ok, I will try one example
A 4 sided body of water (the room).. Rock thrown into water.. (It doesn't have to be rock, jazz or blues will work just the same) But I digress..
Now, here is the part everyone fails to get, the ripples or waves don't move ! They form a peak(s) in one place, and a valley(s) in another.. Peak: Strong signal.. Valley: Weak singal.. You with me ? (I'm not sure right now if I'm with me ?) In other words, as soon as a wave travels from the 1st source, freeze the water ! Get it now ?
But, as we all know, the wave reflects and moves back across the pond (room) creating another 'standing' (frozen) wave.. This 2nd source wave will add too or detract from the 1st wave, boosting the signal, or cancelling it.. Needless to say (but I will) there are an endless amount of reflections going on.. Up down sideways and everything inbetween.. Yeeee Hawwww !!
Remember, this is just 1 rock (sound source).. You try throwing mains, surrounds, a center and a sub or two into that pond, and firing them all up together, you gots yerself a sit-u-aaaaaa-tion..
OK, ok, bottom line, one has to take a few readings around the room, (ratshack meeter/pc/free software) find what's going on with the peaks/nodes, and then fix it as best you can.. Move speakers, move furniture, acoustic panels, etc..
One of the best things you can do to manage a sub is to purchace a Parametric Equalizer, or BFD as it's more affectionately know.. More on that here: http://www.behringer.com/DSP1124P/index.cfm?lang=ENG
Well now, that was easy Time for my nap..
Ta..

LFE ! The rest is just details..