Using 3 DIMM slots 'can' be done but you break the Dual Channel mode. However, mix-matching RAM is a 'bad' no 'really bad idea.' Simply move the fan up higher, the airflow difference won't make a noticeable difference. Otherwise go shopping for new RAM.
You're mixing IC's, still a mix. The worst mix is different manufacturers, and even 2 kits of say 2x2GB + 2x2GB is still a mix and even in the best case neither the Frequency nor CAS Timings are certain to work. In either case of 'mixing' you'll need to manually set the DRAM Frequency, CAS Timings, and DRAM Voltage for starters. Lastly, run intensive Memtest86+ overnight before assuming the mix is good.
There's nothing worst than getting a BSOD in the middle of doing something.
If the RAM is slower e.g. DDR3-1333 on an LGA 1155 then it's possible to find CAS timings that will work.
Q - what kits? ; provide links
Q - what MOBO?
Q - what CPU?
Hmm, the G.SKILL Ripjaws Series 4GB DDR3 1600 F3-12800CL9S-4GBR is hitting the CM 212+ HSF fan?? Move the fan 'up.'
Also, having a bunch of single DDR3-1600 CAS 9 together more than likely will not operate at it's single-stick (rated) Frequency/CAS, and there's a strongly likelihood you'll need to keep it running at DDR3-1333 in a mix and a mix with even (4) four of the same sticks together, and I absolutely would not use 'XMP' in the BIOS. I assume you haven't set the RAM and it's running at Default DDR3-1333.