Set your X and Y zeros with G92. Z zero should remain at machine zero (tool change position).
Bring tool one down manually and touch off work piece. Z will have value of something like -12.3434. Enter this value in any offset you want (lets say offset #1). Same for tool #2 and enter in offset #2.
In your program:
G43 calls tool length offset H1 or H2
G49 cancels tool length offset