I also just started re-building my installation. Its been a while for me too. Definately recommend VPMan Frontend to keep things organised, roms, tables, highscores, screeenshots, launching options, the best feature is notes, that way I can keep track of any changes I made or launching options and problems. Things are a lot easier today to backup in the cloud should your hdd ever crash again.
Maybe a vetran will tell us if they recommend VPMan. Like I said its been a while for me too, years. Feel like I am learning it all over again, only remembering bits and pieces here and there.