All you should need to do is install the terminating jumper on both keypads – assuming those are the only two devices on data bus. Wire each keypad directly to the M1 board, so you will have two wires on each +VKP, Data A, Data B, and Neg terminals. If you want a visual clarification, look in the manual on Page 7. Ignore the M1KP (Keypad 1), M1XIN, and M1XOV devices on the schematic and imagine your setup as just the two M1KP (Keypads 2 & 3).
You said you wired each keypad as a “home run” – so my question is did you wire the keypads with 4 conductor wire or 8 conductor (or Cat5) wire? This will make a difference if you want to add any other devices on the data bus in the future (like your Garage keypad). You should wire all future devices with 8 conductor so you can do the proper “feed and return” to each keypad. Technically, you really only need 6 conductor cable, because power doesn’t need to return, but 8 conductor will give you a connection point to the output and zone connections on the keypads that support it.
If you need more clarification, I can do up a quick sketch. Sometimes it helps to see it visually!