I have written on this subject over the years and will repeat my experience in parting out 40+ 63/64's over the past 18 years:
It is indeed much, much easier to remove the exhaust manifolds with the heads (or complete engine) removed from the car. I have never successfully removed an exhaust manifold that has never been removed from an engine while it is still in the car and would never attempt it anyway knowing what I know now. Assuming you have lifted the engine or removed the head, I do have some good advice.
First soaking the bolt where it goes thru the manifold to is going to do little good in loosening the threads since the threads bolt into the head a considerable distance away from the top where the bolts goes thru the manifold. I have never tried heat, but understand it can help, but have never had to rely on torching the bolts.
On removing the head bolts (and assuming you have the original 9/16" bolts) I always use a 6 point 14mm hardened 1/2" drive socket to back them out. A 14mm socket is slightly smaller than a 9/16" but will fit on the 9/16" bolt. The 6 point 14mm socket vs the 12 point socket will give you a very snug fit. The worst thing you can ever do is slap a 12 point 9/16" socket on these bolts....you might has well go ahead and call the bolt "rounded"! LOL
Also if you have an impact wrench, these seem to back the bolts out with less likelihood of breaking. There is something about the vibrating/hammering action of an impact wrench that backs these bolts out with less likelihood of snapping the bolts off. On the 27 sets of engines I have stripped, I have never broken a bolt off with an impact wrench, however, when I first started stripping these cars, I did break a couple off with a large wrench or socket. It has been my experience that a quick, firm turn on a bolt breaks them free easier than a slow, turning action where you build up pressure. I often free bolts/nuts where I cannot get an impact wrench by taking a LARGE hammer and wacking the wrench and breaking the nut/bolt free. Tthose 5/8" rear drive shaft bolts are a great example of this.
Again, the key to getting any bolt/nut off is to have a tight, firm fit before you do more damage than good. I always use the fact that 14mm is slightly smailler than a 9/16" and that a 11mm is slightly smaller than a 7/16" and almost never use a 9/16 or 7/16 on these old 6 point bolts/nuts.