Your first problem was turning off the sub. It's a "system" that's supposed to "blend" together.
6.5" woofer cones are a smaller surface area than 5x7, 6x8, or 6x9; depending on what he had. But the stock speakers sound like arse, even the bass is crappy.
Your 6.5" woofers will have a more defined midbass output, not boomy. That also makes some people think it's less, when it's actually more realistic.
With all that said, you should have plenty of midbass output from those speakers to "blend" well with the IDQ12, especially with that sub. You still need to dial in the settings.
Try setting the SPX woofers HP 63Hz/24dB, then the sub to LP 80Hz/12dB, and see how that blends. You might need to boost 100Hz one or two on the PEQ; provided you have that option on your HU.
Now overall, neither of those systems has great midbass. Really great midbass with really great midrange will require a 3-way front. But that's a whole different monster to tackle, with install, power, wires, etc.
Since the stock location blends well with a-pillar tweeters, I'd add dual midbass drivers in each door where the lower pockets are, in a sealed custom enclosure. The other option is to put 7" or 8" midbass in the stock door locations with midrange in the kickpanels, but keep the tweeters in the a-pillars to raise the stage. To really make a 3-way system work and blend the best, it's prefered to be fully active with plenty of 31-band EQ tuning options, crossovers, time-alignment, etc. There's a reason I chose to stick with a 2-way front. [
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Your system will work just fine, so keep working with the settings. Double-check those passive crossover jumpers. It's possible you have the midbass cut-off way too high.
What HU do you have?
