I hope someone with more experience jumps in here and helps with some better answers but I'll try. In your zone you probably have some freeze heaving going on. When the ground freezes and thaws it moves, you need a 2-3" base of some sort, sand is the most common here, if you are near rock quarries you might use rock dust or grindings. You need to pack this in and then work your flagstones into it so they set even or level. Then you can fill in with your mulch or whatever.
As for the crab grass, if you're going to have lawn right next to the flagstone you might consider trying to find a herbicide designed to kill crab grass and not your lawn, don't know if that is possible as my lawn IS crab grass with alittle bermuda.
I know that digging out and adding sand and releveling is alot of work, we are currently working on laying 23 Tons of flagstone around our house. It has been going much slower than I expected but DH has promised that as soon as we finish the front yard area he won't be so picky with the rest of this project.
One more thought, I went on a home and garden tour yesterday, one of the homes was owned by a landscape designer who had laid a flagstone walkway all kinda cattywhompus, uneven like, and filled in the cracks with fine gravel chips. He said it made it look old, it did at only l year, and he could spray any weeds that grew with roundup. I'm taking DH over to take a look and see if we can get some more ideas.
Good luck on your project.