I actually don't have problems with that (ok, I'm playing in turnbased mode) but I also avoid areas where I KNOW deadly encounters are there.
F.e I never travel directly from NCR to VC, because there are so many raiders in this desert area. I go a bit west, then north, than east and all I encounter are some molerats. Also the huge desert in the west near San Franciso - everyone knows therea are deathclaws, floaters etc.

More south from this - "mutant land" and then more south again Brotherhood turf. Old city ruins are often crowded with ghouls.
Just don't go from A to B on the map and you're fine, a decent Outdoorsman is also good.