Yeah, a magnet helps. I find it works better on the washers than the nuts. Or put the nut over a long Phillips screwdriver, line up the tip to the stud, and carefully tilt it on, with two fingers from the other hand guiding it.
Here's an idea if you have to do them one at a time (because of the weight). I haven't tried it, though. Hang the exhaust manifold first, and carefully tighten the two nuts on the ends -- these don't interfere with the intake. When you have that squared up, place the in-between metal gasket and the long bolts and the intake, hanging it on the center stud. Add a few washers and get it tightened into place so it's square, but nothing is torqued down yet. Then go ahead and tighten the exhaust-to-intake bolts. Then fully loosen all the stud nuts, and if the ends of the manifolds look even, start over, torquing them incrementally in the proper sequence.