I think what the OP means is this. He has bought or is thinking of buying two stick or ram that are not sold as akit. So in effect they will be two single sticks.
As long as the sticks are of the same frequency and timings then there should not be too much of a problem. Matched kits (either dual or tri channel) simply have the same SPD settings programmed into them and therefore make auto-ram settings so much easier for the motherboard BIOS to set.
Top-end Corsair GTX2 or GTX3 ram is sold as single sticks to benchers.