There is a program that most all iPad users have called GoodReader. It's the 'Swiss Army Knife' for the iPad and it can store files all together and in folders - or however you want them - and can transfer files to and from your PC using either WiFi or USB without the need for iTunes. It's built in web-browser can download files too, something that Safari doesn't offer - except for PDF format. From within GoodReader you can open those files in any app that supports that type of file. Having said that, though, when a compatible app does open that file it makes a local copy that it works on, so the original copy in GoodReader is left untouched. If you want to store the modified file in GoodReader you have to transfer it back there by some means.
GoodReader can also attach several files to an email and then send them using the iPad's native Mail app - something you can't do from within Mail itself. It also gives you the opportunity to annotate PDF files and save the resulting file so that it can be read on a PC or Mac.
It's very reasonably priced indeed - but not free. It's possible there may occasionally be offers and a promotion, though I can't recall one in the last few months for GoodReader. I guess it's so popular and so well respected that the Developers don't feel the need to promote it in this manner.
I now have goodreader after reading the various post on the forum, two things I would like but cannot find how to do are 1) have two documents open at the same time so that I can compare any changes and 2) is there any way to put multiple documents in a particular order in a folder where the sort function is not suitable. (similar to moving bookmarks in Safari)
I don't think that you can do either of these - certainly there's no way to have two documents open at the same time and, as far as I know, there's also no way to order the documents in a folder in a particular way - I don't even know how to do that in Windows
Scottish members are taking over iPad Forum - I see you're in Inverness, I'm just along the A96 near to Huntly - and there's even a Member who lives in Huntly - and three of the moderators live in Scotland...where will it all end.
There's no sort function like Safari's in Goodreader. You either sort by name, date or file size.
If I want particular documents in a certain order, I rename them (maybe put a number in front of them). Then, when you do a sort by name via Goodreader, it'll put them in the order you want.
Re-naming can be done in Goodreader's "Manage Files" area...