As the developer of Birdwatcher's Diary, let me note a few things:
1) If you already have a list or can find it somewhere on the web (e.g., one region, one season, etc.), all you need to create a new list in the software is a simple text file containing one name per line of the species, which can then be easily read into the software (most conveniently using iTunes). When lists are "activated" (i.e., when you select a list from the list of lists that you have stored in your copy of the software), the software automatically appends a scientific name, so that isn't needed.
2) Another way to create a list, which may require fewer steps than deleting unwanted species from an existing list (depending on the number to be deleted!), is to recall a list, and then quickly scroll through the list, ticking the species you want included in the new list, then so to the Lists->Save screen to save the new shorter list. Since deleting a species requires many steps, and ticking only one, this will typically be much faster.
3) Another way to edit a list is to transfer the list to the desktop (a 1-step process using iTunes, although unfortunately because of the way iTunes file sharing works, you have to transfer ALL the lists, but it's still just one step). Now open the list with a text editor and just cut out the lines of species you don't want, save the shorter list with a different name, and read it back into the software.
4) Finally the question of ticking a species which isn't on your shorter list. You CAN click the Edit button, then the + button, and add a species to the current active list. But just as simply, you can go to the Lists->Recall screen, and set it to MERGE mode, and then recall a larger list (e.g., the entire country instead of just one region or whatever). That will expand your list to the larger list, but without losing your currently active ticks (although archiving before you do this is always a good idea). Yes, for the rest of the day you'll be working with a longer list, but the degree to which that slows you down (i.e., takes slightly longer to find a species on the list) is really pretty minor, and it's a more reliable method, because this way you don't have to worry that you don't know how to spell the name of the species.
5) And last but not least, note that lists can consist of anything - not just birds, but mammals, butterflies, amphibians, anything. The only limitation is that, with the latest version of the software, the software knows the taxonomic order of birds, so the list you input can be in any order and the software will re-order it (when appropriate) properly. With other types of creatures, the list must be input in taxonomic order for the software to know that order (to the extent that matters).