On most of my molds I just put them on top of the pot when I start the ifrst mold while I'm getting ready. The mold will heat up fast. When I'm in between pours and molds, I'll put another mold on top of my pot, while I cut the sprues off the first set of jigs. This is the way I do it. There is no right or wrong way, whatever works for you.
Mark as far as magnets and heat. If I remember correctly from an old company I worked for. Yes magnets will lose some of their magnetic quality, when exposed to heat over 212 degrees. Once it loses some of its magnetism it doesn't come back once the magnets are allowed to cool. I don't remember what the magnetic ratio loss was when heated above 212 degrees. I'm sure you can do a google and find out.