In terms of efficiency dual channel is definitely better and since you only have two slots, it seems to me the best solution. I would definitely go with either 2x 2Gb or 2x 1Gb.
Are you talking about DDR2 ram or? It sounds like a pretty old motherboard to me. Perhaps it's not a bad idea buying a new motherboard soon, but yes in that case definitely go with 2x 1Gb.