What is the difference between.....

having all your backlinks go towards your money site or having them go on a linkwheel? Does it affect ranking?

Links to the money site, will help the money site rank. Links to the linkwheel will help the page in the link wheel get indexed, and will help it rank....but as the linkwheel links to the money site, a link to the link wheel helps the money site a little as it make it a stronger link...i.e. ensuring it's indexed, and maybe even ranking.

It comes down to what type of link it is....quality anchor links from articles etc should/can go straight at a money site, spammy comments, bookmarks and profile links may be better aimed at buffer sites like the linkwheel you mention.

The more you build up your linkwheel, the more powerful each backlink from one of your linkwheel sites becomes.