So I have Alpine Type-S 4x6's in the dash, Type-S 6x9's in the sails, and a 12" sub and the sound feels kind of empty. I get good bass, but it's like I hear a major gap in between the speaker range and the sub range.

I think it's lacking what would be defined as 'mid-bass'.

I have a pair of 6.5" Type-S's that I'm going to attempt to put in the dash with a modified bracket to replace the 4x6's. I've also ordered a Kenwood EXcelon (KDC-X997).

Here are the specs of the system:

Headunit: Kenwood HDC-HD545U
Dash: 2x Alpine Type-S 4x6"
Sails: 2x Alpine Type-S 6x9"
Sub: Polk Audio DXi DVC 12" (Wired @ 2-ohms, LPF @ 85Hz)
Sub Amp: Craig Powerplay 500 (250W RMS @ 2-ohms [I think, it's old, hard to find specs])

So would the addition of the Kenwood's 13-band EQ and adjustable high/low-pass filters (a feature which I'm sorely wanting that I don't have) amend my issue, or am I going to need to snag a 4-channel amp for my speakers?

 

those 6.5's and 6x9's are rated like 85 and 80 wrms each, thats were they are going to sound the best. but looking at the description of your old hu, seems to not have alot of the better quality audio stuff, the new one you listed does though. so who knows you may get it together and find its fine to you. but IMO the 6.5's and 6x9's are going to sound much better in that range with an amp meeting the rms ratings.

 

New head unit sounds a lot better. Gonna get a 4x100w RMS amp and hook that up eventually.