I just joined today, but I have ~1800 books on my Kindle and about 5500 in Calibre. When I attach the Kindle to computer with Calibre running it scans and notes which books are on the Kindle. Easy to select & "send to device".
I get alot of epubs, convert to Mobi and they load onto the Kindle. My wife's ereader uses epubs and it loads those onto that one. Fantastic program, I'll be making a donation this weekend.
Incidentally 1800 books on the Kindle has it ~3/4 full, but it really is too many (and not necessary with having Calibre) - reading books there is no issue but moving around on the Kindle seems pretty slow.
Fortunately I have a 23 year old daughter that steered me to Calibre.