No, MC does not use the second source to fill any missing info. The user has to know exactly what he/she wants to do with the second source.
It is hard to communicate a precise message to the users on a dialog window about how this should work. I will give more detailed explanation as I answer your specific questions, but briefly, MC uses "XMLTV channel IDs" that are in guide data file to map a specific program to an MC channel. There is only one XMLTV ID associated with each channel. That is probably where the confusion comes.
Now your specific questions:
Part 1 - No, it does not matter whether a loading method is associated with a tuner profile or not. Each loading method will attempt to put a program in the database by associating it to a particular channel.
Part 2 - I have not figured out a best way of dealing with this. I am not sure why Auto Match does not work, but it should, unless your second data file has channel names that do not match the channel names. That said, when the second mapping dialog shows up, it is absolutely necessary to carry out some manual intervention. You can run Auto Match, but when it asks you whether you want to use new ID or existing ID, you should answer Existing ID, so that you will not undo the mapping done in the first time. Then you should do manual matching of any channel you want to use the second method for, and leave alone all channels that you want to use the first method, even if they appear to have no match at all - because if you make a match for a channel during the second loading, then the data from the second loading will be associated with that channel.
Part 3 - Are you saying you have multiple channels for 2.1 and 2.2 in MC's channel list? Not multiple entries for these channels in the XMLTV data? To clear the multiple channels in MC, go to Manage Channels, and delete all affected channels, and then do a rescan of channels. Or you can examine each affected channel in the Manage Channels tool, and decide if it is a good one or bad one, and delete just the bad ones (this requires you knowing your channel parameters - for ATSC, the Major channel, minor channel, and physical channel numbers).