The colors indicate a 'bank' of memory.
You should use the same size/brand/build of memory in any given bank.
This will ensure that the memory is being used in an interleaved fashion - which is faster.
Fill 'Bank 0' first (they are designated 'Bank 0', 'Bank1', 'Bank2', etc - depending on how many banks your mb supports), which may have been your problem if your MB acted differently when you used the sticks in an alternate bank. (or are you using 2GB sticks in slots that are designed for only 1GB sticks?)
As to what size and how much, that depends on your motherboard.
Mine has 4 memory slots (bank0 and bank1). And it has a max of 4GB.
So I can only use a max of 1GB sticks. (Max memory divided by slots available).