First of all; what version of 5D so you have. There is a version that comes free with you machine; its just an organizer basically.
Then there is 5D that has the other features that allows you to digitize, resize, etc. It goes all the way up to 5D Pro, which is what I have. It comes with small books for each version that gives you a basic plus some tutorials to work on. If you go on your pc under programs then 5D embroidery and you'll see modules, under there it has the same info as those small books plus so much more. I ended up printing them all out and it took 3 big binders to hold them all. There are many ways that people download, store and organize their designs. Mine first go into a folder called orders and each company has it's own sub-folder in it with thier names attached; like order_emblibrary.com. I keep the orginal file zipped in that folder at all times. When you look at the folders in the organizer you can see what is in each one and then save the file to another folder in the organizer with a name that tells you what category its in and a name that tells you more of what it is. I do it this way, keeping the orginal file in a folder with co name because if you ever need to re-download the design you need to have that info, especially for companies that archive files after a certain time.
You would also have gotten a USB stick for your machine and that's where you save your designs to when you want to use them on your machine. Just do a save as on the pc and then chose the drive for your USB stick is in. Check around for classes for 5D; if there aren't any for Phaff then check for Viking; the software is the same. You normally start off learning and designing in the software and then stitching out the design later. A good LQS won't care what machine you have in order for you to take part in the classes, and they normally aren't too expensive. I start 5D Extra classes this month and will end up doing all that 5D has to offer. Good luck.