I have many ebooks as how to guides, instructions etc on my desktop computer. What is the best options to use to store those ebooks so that they are not stored on the actual desktop and taking space?

A simple flash drive will suit your needs well.

Ebooks are typically quite small unless they have lots of images, to me that type of file would be one of the last that I would offload. You could load them all on the reader or a USB stick like Ben said. Burning them to a CD is another option. Put them on a storage site in the "cloud".