You are right. There is basically 2 mib db's in use here. The MIBs.cfg file you mentioned is where UnDP gets its information from. Things like type of counter, trap information, and other such information is stored in this. This can be updated by you by going to the additional downloads section of your customer portal.
There is an internal MIB db Orion uses for all of its internal polling and abilities. This is updated only on updates to the product itself and is controlled by SolarWinds.
As for the UnDP polling intervals, they should be in the UnDP itself. If you leave it blank or default, it should use the default Node polling interval (if its node based) or interface polling interface if its interface based custom poller.