I was as "green" as anyone else when I first got my printer, a Makerbot Replicator 2, and initially used Makerware...but after a couple of weeks, I switched to ReplicatorG, which was supplied with the printer. I was wrestling with getting anything like good results with the default settings for printing small parts...and by small I mean as small as 12mm x 8mm x 2mm!
After struggling to get good quality, I looked around for some guidance....and saw a feature on S3D. I ummd and arrrrd for a couple of weeks...and then took the plunge. Immediately I saw the increased capability of the slicer compared to ReplicatorG. I didn't get quick results, though, as I needed to go through the learning curve of what each of the settings does...and I'm still learning now! But I'm now getting much better quality prints..and I'm now confident of completing a long term project I set myself in March last year....to build a model railway layout featuring the Forth Rail Bridge.
So far, I've printed well over 500 parts for the layout...some fairly simple such as houses, but many quite complicated. And I have to add I'm still struggling to get a few right...but I'm confident that S3D will come good once I get the setting tuned for the part I need to print.
Take a read of this thread on the TalkingTGauge forum:
http://www.talkingtgauge.net/viewtopic.php?f=8&t=123
And the 12mmx8mmx2mm part...its part of a wagon in T Gauge ( 1/450th scale):
http://www.talkingtgauge.net/viewtopic.php?f=11&t=76