First, if you're trying to use tool length offsets, you need to enter the tool lengths into the tool table - simply zeroing the tool does not do this. You can manually enter the tool offsets by entering data directly into the table at Config->ToolTable. Once that's done, you have to apply the offsets, using G43. So, if your tool 2 is 1" longer than your Tool1, enter 0 for the tool 1 length, and 1" for the tool 2 length in the tool table. When you do a toolchange, use "M6 Tn G43 Hn" where n is the tool number. This will both do the toolchange, and apply the correct offset. You can set the Z axis fixture offset by loading any tool, applying its correct length offset with G43, then moving Z to the zero position, and zeroing the Z DRO.
Regards,
Ray L.