Maybe I am not the best to give you advice on this. I got me a printer that came with printing software ("slicer") bundled up with.
In general there are a lot of free tools free tools available online.
For prusa I3 I guess "Slic3r Prusa Edition" is the the way to go http://www.prusa3d.com/slic3r-prusa-edition/
It will work with the clones - see https://www.youtube.com/watch?v=F7JuMa35IjA
For modeling I like using my old 123d by Autodesk but they discontinued the support for it.
My go to alternative is Netfabb by Autodesk. Here you can get a trial or a so call "non-licensed" version (former basic version) which you will get, when you cancel all license pop-ups. It will work see https://www.youtube.com/watch?v=2QRvS9xdNzw
There are a lot of good guides only - I recommend the guides on simplify 3d (I do not use the software though).https://www.simplify3d.com/support/articles/
by Makerbot covers all 3d object needs and has a nice community.
In general .stl files are all you need for modding the objects. Depending on the CAD software you use you will have to covert the objects into proprietary formats to gain access to advanced transformations. Meshmixer come in handy for this stuff.
You will convert .stl files using your slicer into g-code which is the motor instructions and all commands for your printer. Normally you will not be able to use other people's g-code as the commands have to fit your machine and the material you are printing with (speed, temperature, nozzle width, available build plate configuration etc.). It all sounds complicated but it is quiet easy, as long as you start small.
Also FDM printing is not like normal paper printing or CNC. 3d objects have to be designed in a certain way to save material and ensure good printing results. So best to start with stuff that is proven to be printable (see thingiverse).
Hope this advice is of use to you