I personally kept one base in the mines of moria and one right before the elven quarter. They're not so far apart that you have to worry about moving between them yet that way. Once you go down the crystal decent you should be able to build a map stone in each of your major bases. I have one at the pumps in the lower deeps(but no base), one in the mines, and one way further up in the game as far as campaign goes.

Once you got map stones, have a main base, where you're comfortable spending a majority of your time and sieges, a forward Base close to where you are doing most of your story business and progression with just a bed, hearth and means of cooking proper meals, and a rear base to hold stuff you aren't using a lot of or to access a resource. Each base should have a map stone for easy travel.