If you set the number of lemmings to another value, the percentages will be wrong. How it works in-game at the moment is that when you rescue a lemming, the game will increase the "In" percentage by a value supplied in the level data. The number of lemmings is not considered.
So if there are 20 lemmings in the level, you set this value to 05, meaning every lemming you rescue will increase the "In" percentage by 5%.
If there are 3 lemmings, on the other hand, setting the value to 33 means you'll only rescue 99% if all lemmings are rescued. I'd like to fix that somehow. Three ideas spring to mind; either by removing any mention of percentages and replacing it with units (e.g. Number of Lemmings 20, 19 to be saved), by implementing a lookup table, or by implementing a division subroutine, active when each lemming is rescued.
Also, if you use more than 20 lemmings, a 21st lemming will increase the "out" counter to 21, but that lemming will not actually exist. The ghost lemming cannot be nuked, so you have to wait for the time to expire.
About overwriting the space the original levels use, it's very risky to do because the data is compressed. It's fine if the resulting file size is smaller or equal to the level you're overwriting. If it's larger, however, it's very likely that you'll spoil the data for a different level, or maybe interfere with some of the game's graphics, depending on which level you overwrite.