For all the Kobo newbies, here is a mega-thread with all the tips and tricks so far. If anyone learns any new tips and tricks, please post them here.
1) USING THE KOBO WITH THE KOBO SOFTWARE
Create an account at the Kobo website, or log into your existing Kobo account. Click on your library. Unless you have done some fiddling already, all the books you have bought will appear in your 'I'm Reading' list. This is what will sync to the Kobo.
If you have some books you have read already and/or don't want to syn to the Kobo, click the checkmark beside them, then click the delete button at the top of the list. The books will still be in your purchased books area but will no longer be on your I'm Reading list.
Plug in the reader. Open the desktop software folder and install the software for your type of computer (Windows or Mac). Launch the software, log into your Kobo account. Click the sync button. The books will sync onto the Kobo Reader.
Books loaded onto the reader in this way will not appear as files if you double-click on the device icon in the desktop. If you want them to appear on the device and be editable, you will have to load them through other means such as Adobe Digital Editions or via drag and drop.
2) USING THE DEVICE WITH ADOBE DIGITAL EDITIONS
Log onto your Kobo account on the website. Go to your library. Click on the 'download epub' icon and when prompted, save the file to your desktop.
Go to your desktop and right-click on the .acsm file. Choose 'open with Adobe Digital Editions' and open the file. While you are in ADE, authorize the Kobo reader to your account.
You should then be able to drag and drop books from your list in ADE onto the reader icon.
Note: If you are downloading library books, it is the same procedure. Sve the .acsm file and open it using ADE.
3) USING THE DEVICE WITH CALIBRE
Make sure the Kobo Reader is plugged in. Have Calibre open and make sure you can see the 'Kobo Reader' icon on your desktop.
Select a book from your list. If it is not in epub, convert it using the 'convert' button.
Right-click on the file name. Choose 'open containing folder.' Drag the epub file onto the Kobo Reader icon on the desktop.
4) FIXING AN EPUB WHICH WILL NOT LET YOU CHANGE THE FONT
MAC users: Download a program called ePub Zip
PC Users: Download a program called Free Zip
Click on the epub file. Click on the file name---it should become highlighted so you can edit it.
Change the part that says .epub to .zip.
Double-click on the new zip file. It will make a folder.
Open the folder. Find the file that says stlyesheet.css and delete it. (IT may be inside another folder like the OEBPS one.
MAC Users: Drop the folder onto ePub Zip and you're done.
PC Users: Use Free ZIp to make a zip file. Highlight the file name and change the .zip to .epub and you're done
Drag the new epub file onto the Kobo Reader icon.
Note: Files edited this way will allow font adjustment, but may lose other formatting such as full justification
5) DELETING THE PRE-INSTALLED BOOKS
Srid outlined the procedure here