Chris, I've never known of any program or affiliate considering two tier MLM. Two tier is a standard in affiliate marketing. Affiliate referral programs and their resulting commissions are a popular method for quickly growing a budding affiliate database, so I don't think there is a fear of being mistaken for MLM.
Joe, as for your questions, Linda is right on with "depends". There are no definitive answers. It is mostly trial and error and can become frustrating. Just keep in mind that it will not happen overnight and is as much a job as any 9-5, if not moreso. My suggestion is to research as much as you can. Keep your eyes on affiliate marketing newsletters (a co-reg deal with one of those newsletters would also be a good way to get your program seen) and forums and
keep your chin up.