Hi! I'm pretty new myself, and just setup my PRST1 also [switched from KoboTouch].
I use Calibre for the reasons you mentioned, to orgarnize my library the way I like it. I would suggest you setup Calibre as suggested in the thread I've linked below and then use 'tags' column to organize your collections the way you want. Good luck and I hope you enjoy your T1 as much as I am!
PS. the full instructions are in post #15 of this thread, very detailed and helpful!
https://www.mobileread.com/forums/sho...d.php?t=169043