I cant speak to the change from MDB plus to other software as I've only edited this years and last years version and have always used a mixture of SQLiteStudio but mostly I use DB Browser which can be found here -
https://sqlitebrowser.org/dl/That is the most user friendly and intuitive when learning I think.
I terms of how to do edits once you've got the software downloaded, you dont actually edit your 'save' which I think is what you have mentioned but you edit the database itself so that when it creates ANY new save it will use the edits you have made. I actually go into a fair amount of detail at another users request about how I do the editing for the updated rosters etc that I put in the mods section for DDSPB. You can read through that thread and I think you may find some of it helpful -
viewtopic.php?f=328&t=34064Just so I understand the situation fully, are you looking to make edits to the real world mod/nba? Or are you looking to make these edits to a fictional universe generated by the game?