Hey brazensol.....unfortunately, you'll have to use 2 separate channels when adding the MBQuart drivers. Because the JBL drivers are so different in design than the MBQuart drivers, you'll find the power setting on the amplifier that works good for the JBL's won't work as good for the MBQuart drivers and vice-versa. So, it would be hard to get the 6 JBL drivers to behave the same as the 6 MBQuart drivers on the same circuit. Hope this makes sense.
Now, if you bought 12 of the MB Quart drivers, then yes, all of those could be powered by one channel of the 6000 since it would have enough power for all 12. Or, if you bought 6 more of the JBL's that would work with one channel also, but it sounds like those 6 extra JBL's won't fit if I understand correctly. Also, the MB Quart drivers are dual voice coil drivers which makes wiring a bit more flexible to match impedance loads for different amplifiers. If this is the path you choose, just let me know and I can help with wiring those 12 on one channel of the 6000.
For 2 channel wiring, just keep the JBL's like you have them now and wire the other channel with the 6 MBQuart drivers as shown below. This will give you ~5.4 ohms for that channel which is pretty close to the 6 ohms you have on the other channel with the JBL's.
Regarding the hole locations, since you have a 2" thick platform, it's plenty rigid to accommodate the extra holes without much concern. If it were me, I'd probably keep the drivers about 2" from each other for a bit of safety factor if that works OK for your chair clearances.