Currently I am storing my bottles in the crates at a (about) 20 degree angle (bottles are upwards!).
Does the way of storing the bottles affect something (and how)?
In general, you just want to store your beer bottles standing upright. For tons of detail on bottle storage, BeerAdvocate has a great guide, but in short: storing a standard shaped beer bottle upright minimizes the surface area exposed to air in the bottle, slowing oxidation, and preventing spoilage. Additionally, in the case of unfiltered or bottle conditioned beers, it's highly desirable that any yeast settle at the bottom of the bottle - and not anywhere else.
I've looked into this quite a bit; I was thinking of building a beer rack as a winter project. However, All my research tells me that beer should always be stored upright, no matter what variety, unlike wine which is best stored on its side. Beer advocate has an interesting article on the subject. For corked bottles, one does not want to impart any off-flavors from the waxes and other chemicals on the cork. For proper aging, it is also best that the yeast be allowed to settle on the bottom of the bottle.