When I'm building my levels, I'm always sure to save to the ROM before clicking the arrow to work on the next section. Sometimes when I do this and go back however, the section I was working on is erased, and has a totally different layout. When I go back to load the ROM so that I can re-access my built area, it still shows the new layout, so it's as if I never did anything!
Someone please, either give me advice, or tell me of a better SMB3 editor to use.
Does it all look garbled? There's a chance that you could have overwritten the level data of one level when you edited another one. The common case is when someone edits 1-6 and adds more data than what was originally in it to find that 1-4 was overwritten. I'm not 100% sure if this is necessarily your problem though.
Better SMB3 editor? SMB3 Workshop works fine. Overwriting level data to make levels longer is fine as well provided that you keep a log or something of whatever you overwrite so that you don't write to it a second time. You can input custom starting ROM offsets for enemy data and level data in SMB3 Workshop, so if you overwrote one level's data to make another one longer, you can still use any remaining space that you didn't use for another level; just use a hex editor like the one in FCEUXD, locate where the last level ends, and create a loadable 9-byte level header (since it was originally another level's data, 99.9% of the time it would be junk data for a level header; just copy the level header of another nearby level for now because you can always edit it later). Record the starting point in the ROM for this new level that you want to edit and load it up in SMB3 Workshop. Whenever I edit levels at different offsets, I also count the number of free bytes I have to work with in the hex editor so that when I'm editing the level, I know where I have to stop so that I don't overwrite another level's data.
If that doesn't help, try posting some screenshots so that I or someone else who beats me to it might have a better idea what the problem could be.