https://github.com/alexrj/Slic3r/wiki/Documentation is very useful...here is what I do....
Generally I prefer .2 mm tall prints, with .15 density honeycomb infill, and concentric top/bottom fill. I keep my speed settings more conservative than I did when I first started printing, but as fast as possible; the main theme with the print speeds seems to be that you don't want the motor to start skipping (that makes sense lol), resulting in the possibility of a clogged nozzle from the filament siting in one spot and baking in the PEEK...so I am for 80-120mm/s max for any section atm...that's a good rule of thumb on a SD, but I typically go as high as I can on each area when I did my setup. The acceleration software normally handles bigger part areas well (if you are printing one really small part...you might have to manually slow down the printer or add a fan)..you can go way higher on "non-printing movements" I keep mine around 200 for these movements (you can turn that up pretty high...I gone as high as 500 with no problem other than it might whack the crap out of your hand if you are not careful...or slam into a non end-stopped side and crack something). I personally rarely use support (as I dislike cleaning up my parts afterwards, they should come out looks great imo). I do keep on the skirt with 2 passes at least 4 mm away from the print; I sometime use brim on small-tall objects. The perimeter's section is very important as that determines if you even have enough depth to see all of the detail (if it has detail) of a print..e.g. yoda needs X perimeters so his skin textures are all correctly drawn... If you had something like cup and you wanted it to be very thin you could set it to 1 perimeter, adding more would add to the thickness of that cups wall. Top and bottom are exactly what they sounds like...for cups don't use top layers obviously, etc.
I calibrate my extrusions section as IAN's site suggest, but then I set everything back to zero when I have the firmware setting adjusted and let the Slic3r software do the work from that point.
Filament settings - use a "bridge calibration" to find the optimal temp for your specific filament. it will give suggestions to tweaking your retraction speeds, after you interpret your results.
Printer settings - Just make sure you have the needed retraction settings correct...you can also set Start and End G-Codes if you want...there are some nice pre-print processes you can preform, as well as automated part removal and special re-homing instruction (I make my extruder @ home a different than the default path just because I added a larger fan to the extruder and don't need a collision with the z-axis guide bars...I have a settings file I can post, but once you get the general idea of what each of those sections do in Slic3r you will understand what went wrong with a certain print and even better yet you will know how to optimize your settings to get different effects. (like cutting away infill and thinning wall settings to print cups)
Hope I was not repetitive and this at least gives you a little better intro into what is going on with all those setting (I know they seemed daunting at first to myself also, but it won't take long until you can tweak your prints like a master)
