This specific issue was with v10 of ArcGIS MPC. What we did at v10 was produce an amp file (which was xml at v10) by adding operational layers from the mobile caches. This put all the config in the amp file, including the checksum and then all we did was edit it to add the server path and protocol.
I'm not sure if checksum is required in the amp file (a JSON file) at v10.1.1+ as when we add an operational layer from mobile cache, it no longer puts the checksum in the amp file. I've not tried it, so I don't know for sure, but you could try just specifying:
"mobileServiceUrl": "<your url>",
"webClientProtocolType": "BinaryWebService",
for the cache in the JSON.
Hope that helps.
John