Quick answer: Calibre
I've been using Calibre (
http://calibre-ebook.com/) for ebook/library management since my Kobo WiFi in 12/10 and Kobo Touch in 7/11 and can't imagine organizing my ebooks any other way. Definitely superior to Kobo desktop app, Adobe Digital Editions, etc.
With Calibre up and running, plug your Kobo into the USB port and wait for Calibre to show your library. Import ePubs, PDFs, Mobis, etc. via Add Books (the most onerous operation is navigating to wherever you downloaded ebooks). Clean up the metadata a bit. Then highlight and click on the Send to Device icon (you can select main memory, card A, etc.). Under the same icon, Eject Device, wait for the Kobo to process these "sideloads" (ie, they didn't come via Kobobooks.com or ADE). And Bob's your uncle.