Hey there. I think I may have made the interface a little confusing, but you check the boxes for the games you want to EXCLUDE. So if you don't want to play SMB1 and LL, you'd check the boxes for those games.
I couldn't recreate your 1P issue in bsnes 115. Do you have the seed for the rom that wasn't working?
Edit: Changed the UI to make more sense. Leave the games you want to include checked, uncheck the games you want to exclude. So you can now just uncheck SMB1 and SMBLL.