Tinks, I'm expanding my pond, too (next week, hopefully), and your idea was pretty much exactly what I was kicking around for a while. A SHORT while. I decided two ponds linked that way wouldn't work well.
From what I've learned on AP, it is possible to seam two liners together. But it's better to do it when both sections are new and dry and flat on your driveway, not in place in the pond setting, and dirty and on an unlevel surface. Also, is it John? from Garden Endeavors said there's a good chance tree roots will find the seam and work their way into it, causing a leak.
Also, you have to be sure the water in the shallow pond does not become stagnant, and has a way to flow back and forth into the deep pond. So your wall between them must be lower than the outer sides of the pond. Too much engineering, and too weird of acrobatics for the liner.
What's wrong with the pump setup you have now? Why do you wnat to move them? Just to make them easier to lift out of the pond? Then how about raising them up on milk crates. Fish and water can still flow through, but the pumps would be easier to pull from the pond.
Take your time, think it through, and make sure you've examined every possible method, before you start to dig. Oh, and, this time around, I'm hiring guys to do the digging. Busts my budget, but that's better than busting my back. Are there some college kids around? farm workers out of work now that it's winter?