I'm a newbee, but came up with a simple system for myself which is *very much* similar to what other people use so I sure ain't taking credit for it.
I nailed and glued two scrap pieces of 1/2" thick plywood together and then cut the sandwich to a dimension so that it will fit inside of the frames and leave maybe 1/8 to a 1/4 of an inch gap between it's edges and a frame. Once the foundation is secured under the wedge and positioned in the bottom groove (I'm used wedge top bars) I carefully lay the frame/foundation onto the 1/2" plywood sandwich with the wires on top of the wax. The weight of the frame presses the wires against the wax. I have some old test leads off of a volt meter that I have attached to the leads on the battery charger. I rest each hand slightly on the end bars putting slight pressure against the wax with the wire spans. I have the leads in my fingers and slowly "tap" them against each end of a span of wire...tap, tap, tap.... When I see the wax *just* start to melt I stop...the melting will continue for a split second. If I see a stretch towards the middle that might not have embedded very well I can tap the probes on the wire on either side of this unembedded area....tap tap.
Keeping the heat on the foundation indeed is a good way to cut it...makes a nice slice!!! Ask me how I know!!!
It will just take some experience and you'll have it down pat. As for the holes, if the foundation is secure and not falling the bees will probably fix it up. I had a frame that had been "sliced" and when I looked in the hive a few days later I could see it kind of gapping open. Several days later the bees had drawn out the foundation and I couldn't tell where the slice had been. YMMV, of course.
I haven't got to the point where I embed the entire frame at one time...I figure I'm not a commercial guy, nor even a sideliner, so I've got time to go a bit slower.
I personally would just keep the wax on one side of the foundation...it seems it would make it easier to embed with no flipping sides. But, all I've done is medium sized frames so I don't have experience to share on the deeps.
Good advice from these other guys.