The activations are not based on FS version, they are based on the PC.
So, if you use 1 PC, and have both FS9 and FSX installed on that one, you'll will have 6 activations.
If you have 2 PCs, one with FSX the other with FS9, you will have 6 activations in total. For example, if you consume 3 activations on the PC with FSX, you'll have 3 left on the other one.