The analysis will be very similar in the broad sense whether you perform it in Galaxy or through other methods (line command, etc). So if you have a publication or other analysis that you want to replicate, check to see if those tools are on http://usegalaxy.org or in the Tool Shed for use in a local or cloud Galaxy. If available, or you want to write your own tools wrappers, then you can execute the analysis in Galaxy.
For the specifics of using the RNA-seq tools already wrapped for Galaxy, the top of the Galaxy Support wiki has links to many resources. The NGS 101 has an RNA-seq example and the Learn section of the wiki has several. Reviewing these tutorials should help you to understand the overall processing and tools involved. In combination with those tool's documentation, these will help you to understand what specific tools are doing and how to tune parameters.
If you have problems with a particular tool and cannot find the solution here or in the wiki by searching prior Q&A, please let us know by posting a new question with the details, or you can send in any errors through a bug report.
Thanks, Jen, Galaxy team