I'm installing the Might and Magic and Master of Magic games and was wondering what DOSBox version do I want to use? I tried downloading the latest from their site and it wouldn't recognize it. Is there a certain version I want? Or just take the one GOG supplies on the installation?

I usually take the default thing, and only upgrade whenever the provided version does not work. They bundle it for a reason ;-).

The one that gog provides is sufficient. What I mean is, I had no problems with either of these games.
Misread the game titles. I only tried the MoM, and it works. If you think that Might and magic doesn't work well because of the DB version, just do as TheCowSaysMoo says (funny if you read it out loud =) ).

The trouble is that the GOG installer seems to only recognise the version of DOSbox installed with the game and lower, but none higher.
The easiest way is to just install the bundled version, and then replace the bundled DOSbox with a newer version if you wish to upgrade. It should rarely be needed though.

It's actually best to use the GOG supplied ones I would think, since often DOSBox updates break games that were compatible with it before. I know I have had to hunt down an old version of it to run certain games.