Shane (@NC7C) got me hooked up with Ham Radio Deluxe for my primary logging. It's absolutely lovely. All of my contacts are logged inside of that and then that facilitates the upload to QRZ.com, eQSL.cc, LOTW, Clublog, etc.
For me, it was a life saver when I accidentally deleted my QRZ log book. I was able to open up HRD and just "sync" it back to QRZ and instantly, my entire log book QSO's & QSL's was restored.
The WSJTX "integration" was seemless to Ham Radio Deluxe and it is "fully automatic" when a RR73 or 73 occurs during a WSJTX QSO.
What do you use?