You should be able to go up to 4000x4000 (some systems even 8000x8000) for the raster maps. They will be a little slow to load, but even if you split it up you still have to load them. Personally I'd go for large ones covering as much area as you can.
Yeah, waypoints are a good way to get them calibrated. Doesn't need to be corners -- any landmarks should work.