I have an IB with with the PE IB15's. I originally purchased these when the 15in sub market was dry. There were good subs on the horizon, but no materialized dates. The PE IB15s are a decent sub for the money and I've made them work for me. However, if I were starting over I'd definitely shop around. The PE IB15s are acceptable for what they are, but there are plenty of higher quality subwoofers out there.
To comment on wanting to add subwoofers to your main channels... I'm running Polk Audio's cs1000p and rt2000p's for my frontstage which all have built in subs. The cs1000p has two 6.5" subs and the rt2000p's have dual 8" subs in them. I'm listing my setup because I didn't always have a setup like this. I started out running bookshelves and went through a series of upgrades over a year to get where I'm at now. When I had any other speaker I ran them as "large" since it produced a more full sound. So I concluded that if I got bigger speakers to produce an even more full sound, that the system would sound better and better. However, now that I have a frontstage that responds well I've changed my mind about this. Running my mains as "large" muddies the sound and detracts from the details that are in movies. Most of the "surround sound" you hear is in the higher frequencies; raindrops, things panning left to right, gunshots, etc. So after building a really good subwoofer, crossing my main channels over to it, then EQ'ing the subwoofer to blend with the mains, I prefer this configuration. I might have lost a little bit of bass directionality, but that would be nitpicking the setup since overall the clarity and response of the system is much improved. In summation, I'd make sure that I had a capable subwoofer before adding subs to the main channels. This is where an IB configuration would suit you well since it seems you're halfway there.
If you are still going to build woofers for your mains, then definitely bring them in closer in proximity to your bookshelves. I was going to build woofers before purchasing the front stage I have now, but I was concerned of a few things: How to cross them over properly to the speakers they are coupled with, using plate amps could mean you're using a lower quality amp than what the other speakers have, does the sound quality of the woofers match that of the other speakers, and how does placement of the woofers affect the sound quality of that channel's speaker system? To me, I was introducing several problems and it seemed like I needed to know speaker theory to solve them; perhaps I was overcomplicating the issue, though. So if you build the enclosures, add power, cross them over properly, how much money would you have invested in them? Would selling your bookshelves and couple those funds with the woofers you would build allow you to buy higher quality speakers for your front stage? And perhaps those higher quality speakers would have the frequency response you're looking for, too? (Those questions are rhetorical, BTW.)
Hopefully I'm not confusing the issue, or hopefully I'm not telling you things you already know. Perhaps my experiences could help you out.