If you can run all 6GB, do it. It may boot it may not. Go into the BIOS and try to manually set the speeds, the voltage, and the 5 important timings (tCL - tRCD - tRP - tRAS - tRC - command rate). If it boots up at decent speeds and timings (such as DDR2 800, 4-4-4-12-23-2T) then I'd definitely keep it. Vista loooves RAM, and as previously mentioned speeds and timings aren't going to impact performance much as long as they're DDR2 800 or faster and 4-4-4-12 or 5-5-5-15. But remember, when running RAM of different types, the following problems occur:
(copy/pasted and modified from my answer to a thread about 2 down from yours
Can you combine RAM of different types? Probably, but here's what is important to know when combining different IC's:
1) All memory modules must run at the same speed. This means your overclock is going to be limited by the weakest module.
2) All memory modules must run at the same timings. This means if one set can run 4-4-4-12 timings at 400MHz (DDR2 800) but the other set needs looser 5-5-5-18 timings, it all has to run at 5-5-5-18.
Now that all kinda sucks, but here is the deal breaker for a lot of people...
3) All memory modules must run at the same voltage. If one set needs 2.1v to run at the current speeds and timings, but the other wants 1.8v, you could be in trouble. Setting the voltage to 1.8 could undervolt the 2.1v kit, causing it to not work at the given speeds and timings, but setting all memory to 2.1v could fry the 1.8v kit.