I'm not trying to be arrogant or fanboyish, but I consider myself quite versed in the ways of nzbs and the like, and all the problems people experience here are new to me and sound really confusing.
First of all, Sabnzbd definitely remembers preferences. I've used stables and betas, on both Windows and various GNU/Linuces, and never had a problem. I did have a problem with Chrome not saving a pref once because it failed to authenticate my Sab password after I'd changed it on a different computer. This is a Chrome issue, not a Sab issue. Firefox worked.
Secondly, why are you downloading separate RARs? Isn't the point of nzb files to get a handy package of all the RARs you need? I'm confused.
Also, deleting the RARs after successfully unpacking is a very welcome option in my opinion, and it should definitely be the default. The keyword here is "successfully". The only time I ever see RAR files is if pieces were missing from usenet and Sab couldn't get enough repair blocks. Then I look for PAR2 files and retry from within Sab if I find them (if not, I'm screwed no matter which app I use). I do a lot of automated downloading, and keeping RARs would fill up my HD in a week. I literally never have a problem with setting Sab to autodelete RARs.
Did these problems arise because you downloaded half the FE with one app and half with another?