Me personally, I would separate the jacketed and FMJ's from the really flattened out or solid lead bullets.
Then I would use a either a sledge hammer dropped on top of the FMJ's or a long handles pair of wire cutters to split the bottoms of the jacketed ones. This will do two things, first it will give any moisture trapped inside an escape route once it starts to heat up and turns into steam. Second, it will allow the melted lead an escape route, so that it doesn't build up pressure inside of the jacket and either burst or squirt out in a superheated stream.
Either of the above things can be VERY bad in a half or full pot of heating lead. The bad thing is you cannot dictate just when each one of them might start doing something like that and if your opening the lid of the pot just at the wrong time, your going to get either sprayed with molten lead, or worse some water manages to make it into the molten portion of the lead which causes it to explode. (AKA- The Tinsel Fairy)
When you heat up your scrap bullets, start with a cold pot and do them in small 10-20# batches. This will give any moisture in the jackets a chance to steam off before everything is submerged in molten lead. I would not mix the jacketed with the lead or cast bullets when doing this part, due to the above reasons. Also DO NOT ADD any jacketed bullets to already melted alloy, as it can possibly create one of the situations mentioned above, resulting in a nasty burn.
As already mentioned, wear some protective clothing while doing this. It might be a pain to do so, but it is a WHOLE LOT less of a pain than you might receive by not doing so.
Hope this helps.