Don't worry, you're not alone
Though I first solved the levels on the Mac, where the solution to Part 1 is as simple as digging into that holding area and bashing across. Part 2 is only slightly more complex: bash into the wall, dig deep enough to hold the lemmings, resume bashing.
I had a rude awakening when I first played the Genesis version and found that this didn't work! The solution I eventually found was, indeed, to use the holding area as it's meant to be used -- and I solved Part 2 by constructing a similar holding area just inside the wall.
Incidentally, Parts 1 and 2 being non-duplicates is necessary to complete the pattern: 40 pairs of duplicates and 40 individual levels. Also, except for We All Fall Down, every duplicate pair has one member in the first 43 levels (up to Tricky 13) and one member in the last 77.