I've done few double sided boards with toner transfer, but not too many. In my opinion, double sided toner transfer is more trouble than it's worth, but it can be done.
A common problem is that the patterns come out of the printer slightly compressed or stretched in one dimension so that they don't match up perfectly. So, you should print both patterns on the same sheet side by side. Then cut out the patterns and line them up to make sure that they can be perfectly superimposed. If they're okay, then you can tape them together in position on two opposite ends and slip the PC board in between. Be very careful as you feed it into the laminator. Hold it tightly as you feed it into the laminator to make sure that things don't shift. Like most things, it may take a bit of practice.
Another option is to do one side at at time. Completely cover one side of the board with resist (I use fast drying spray lacquer), and apply the toner transfer to the other side. Then etch it. Remove resist from both sides. Drill two of the through holes to use as alignment guides when attaching the second toner paper. Don't forget to cover the already etched side with more lacquer. It doesn't always work perfectly, and I wouldn't try to do intricate designs.
There are a few black marks left on the transfer paper, but not as many as missing from the board.
Are they:
Poor laser printing?
Not enough heat?
Not cool enough before separating?
With the paper that I use, I've never had to use any physical force to separate it. I just drop the board, with paper attached, into a dish of soapy water, and let it sit until the coating on the surface of the paper dissolves and the paper floats away. This may take a half hour or more, but there's never a risk of untransferred toner. None of the toner remains on the paper. It all transfers to the board.
Also, toner may not stick to the board properly unless the board is scrupulously clean. Make sure it's clean and degreased before applying the toner. Once the board is clean, don't let your fingers touch it. Handle it by the edges only.