most of the patches on the cd are d/l able from the websight, in the free download area. most are usable with PA and the original version.
afaik the main thing the cd has that is not d/l able is a lot of artwork for walpapers and such. all of the game play files are available in the $5 download, or for free else where on the site.
after you install just go to the PA forum, at the top of the posts are 'sticky posts' that have any patches available, and why you'd need each one. (for example ther is a very important 'torpedo room' patch that fixes a crash on certain boats. this came out about 3-4 days after the PA patch so I'm not sure if it's on the CD's (unless they are making them as ordered instead of doing a bunch ahead.
with the $5 download you recieve, the PA patch, the hi-rez patch, and the needed files from destroyer command to make the new patch work.
there is suposed to be soon (if it isn't ot already) a free version of the PA patch out, but it doesn't have sound, hi-rez, or the destroyer comand files. so you'd have to have detroyer comand to make it work and you'd still have low-rez, and no sound.
as far as a back-up goes. there is no reason you can't save the files on a cd once you d/l them, I did.
since I get a fairly good d/l speed and the artwork wasn't a big issue with me, I went for the $5 deal. I just pay-pal'd them the $5 and they sent me the download info a couple hours later. very simple, no problems at all.