Currently, you have to assign a macro to a button (either Omnimouse or Fragpedal) to get it active and working while you use the configuration. Even though the macro might, like in your case, just set up keyboard keys with macros, it has to be assigned to a button. Buttons are where you "hang" macros, even macros that don't have anything to do with a button. For instance the Wiggle scroll macro just uses mouse movement to scroll it doesnt use a button, especially the one its assigned to.
SO. the trick is to set up your configuration so you have enough button assignments to "hang" all the macros you want to use. The trick with the Omnimouse is use a Shift button to create an alternate button setting for each button, and use the shifted set to assign the macros for the keyboard and so on. You lose one button for the Shift function, but you gain 7 more (the shifted settings minus the button used for the shift + Lift. You can assign a different macro to each lift event of each shift state. You never actually use the Shift button, but the macros on the shifted buttons will all just work (assuming they are keyboard macros).
The trick with the Fragpedal is to use the virtual buttons to host the macros that setup keyboard keys with macros.
Another thing to keep these keyboard macros small in number is to use functions like the WaitForKeys4 and 8. These functions can wait on 4 or 8 keys, effectively giving you 4 or 8 macros in one.
There is a sample macro in the new macro pack that you can test this with. Its called ToggleKey I think. Assign it to a button, and it just makes one of the keyboard keys into a toggle key. Its an example of a macro that has nothing to do with the button you hang it on, its for a keyboard function.