Have a look at the tutorials on transcriptomics from the Galaxy Training Network: http://galaxyproject.github.io/training-material/topics/transcriptomics/
There are two tutorials there, one for reference based RNA-seq analysis and another for de novo transcriptome reconstruction RNA-seq analysis. All of the tools in the latter can be used on useGalaxy.org .
These tutorials have step-by-step instructions for running the tools and screenshots to guide you along the way.
Best of luck with your analysis.
If you have links to the files you can add them with the "Paste/Fetch data" option in the upload portal. If you would like help setting up a FTP connection, please see this guide: https://galaxyproject.org/ftp-upload/
Thanks for using Galaxy!