I have had my shop up for almost half a year and just recently started making sales. I spend more than half the time on actual artwork and uploading images to my store.
I have been thinking about setting up an affiliate store. Still I am wondering if its worth getting into. Can one make a substantial amount of money from something like this?
And if I do decide to go with it, I am not sure how to begin. Should I use my own store to put up affiliate links up or is it better to build a whole new website for it?
Can someone give me advice on the best way to start? Thanks!

Whether it is worth your time depends entirely on what motivates or demotivates you. There is virtually no relationship between being an artist/shop keeper and being an affiliate. They are entirely different jobs, with different tasks and different approaches. Your CafePress shop must be entirely separate from affiliate marketing. To make any reasonable money as an affiliate you will need an outside web site and you will need to market that site. While you may include your own works along with what you are marketing the mind-set is different. As an affiliate you are selling other people's products and you will need to promote and showcase them with enthusiasm. If you don't like marketing then the affiliate stuff is probably not for you (although I guess I give lie to that statement as I loathe marketing but I sell other people's stuff at a higher rate than my own).