Thanks for the advice on evernote! Just DLed it and I'm working on that guide as of the end of this post. I'll send you a copy of the post as a PM so you could give me your two cents before posting. Also, I am a Linux user, so you could help a lot by providing the screenshots for PC users!
@ whoever is moderating this section, I'll make your life easier.
To conclude our thread, the answer to our question is as follows:
The is no 'proper' directory to send files that you want to view in iBooks. However, what you could do is download ifiles to your iPad, and have the app open it for you from whatever directory you've sent it with.
As mentioned above, there will be a guide posted in the How To section of this forums on to explain what procedures are necessary in order to send/ recieve and then view files on the iPad.
Mr/Ms moderator, you may lock this thread as it has been answered. Thank you everyone who has contributed!