Grats on your reader! I'm sure you'll love it.
Like Asawi, I also prefer the Sony covers if you can still find them at reasonable prices. And also like Asawi, I first got the lighted cover, then also the regular that I use the majority of the time when I know I won't be needing the light. If you can only get the regular cover now, good light options that I also have and like are the
Lightwedge Arc Light (especially since it's rechargable and uses the same charger or usb cable as the 350), or the
MightyBright TravelFlex (takes only 1 AAA battery). Both are very light, both will last roughly 24 hrs of use or so.
PRS+ and Calibre aren't "essential", but they will both greatly add to your enjoyment of the reader and are highly recommended. Asawi gave you the PRS+ link, you can download
Calibre here, and we have a very active Calibre forum here for even more help. Be sure and check out at least the 2 basic Calibre videos, it will show you ways to use it that you might not find just poking around it. PRS+ also has it's own thread in the Developers section if we can't answer something here.
You'll need Sony software if you want to buy from their online store, and to update the firmware. Other than that, I never use it to manage my library at all, Calibre is much superior to it.
Epub of course is the preferred format. Other than that, depending on your eyesight, which font you find most readable for you, there are a lot of recommendations about that. I haven't run into many badly formatted books that required reformatting to get rid of margins, but should you need to do it, Calibre makes it simple and quick... convert it with your settings and send the reformatted epub to the device. My preferred font is LexiaDaMa, and there are others pretty close as well, you'll find threads devoted to favorite fonts here. You pretty much need to try them and see which one you prefer.
PRS+ is the only one that installs on the reader itself, and yes, you can reverse it to go back to original factory firmware. Calibre is installed only on your computer, and then you transfer your books over to the device through it.
Edit: Just saw your other post you snuck in while I was typing. The .mobi format is for Kindles. Sony readers will accept .epub, .pdf, .lrf and .txt, (possibly Microsoft Word, RTF and BBeB also but I've never tried any of those to confirm how well). But .epub is the usual preferred format for ebooks. Most libraries only use .epub format, some are expanding to other formats now.