My 1x12 is equipped with a doughnut. I found the 3/4 inch foam to take off too much top end so now I'm using 1/2 inch foam which I find to be the sweet spot - takes off some of the nasty top but doesn't cut into the presence too much.
How you would go about micing it obviously depends on a whole load of variables, the cabinet, the speaker, the kind of tone you're recording, etc. With the doughnut you can obviously get the mic quite a bit closer to the cabinet than without one, which is good if you're using a dynamic, but apart from that, my mic positioning techniques w/ a doughnutted cab aren't any different to those without.
Personally, I like to put a condenser about 4-5 feet away from the cabinet, facing the cabinet at an angle, and then for some sounds I'll also add an SM57 in the back of the cabinet and mix the two appropriately. When mic'd, the back of the cab gives you a lot of low end punch and quite a bit of presence, and can sound nice in the mix if you can sort out any phasing issues.
I really hate close micing on any kind of distorted sound, even with a doughnut it sounds so harsh and fizzy and thin its unbearable and sounds worse than going direct in, which defeats the point of going through the hassle of micing the cabinet. It's absolutely shocking to me when I watch gear demo videos and they slam an SM57 right on the grill cloth - you can't even hear the character of any equipment like that, it's just disgusting.