Bob,
Cylinder up or down does not affect much to how the engine runs, actually you can expect more running symmetry problems with a side-mounted engine. But differend engines behave in differend way, it's not possible to give an universal answer.
When cylinder points up there is of course cosmetic issues but you may also face problems with vertical c.g, tank position and possibly landing gear height.
For other than cosmetic reasons I have ended up with cylinder pointing 40 degrees down.
Lauri