I think the only things that matter for the engine placement are CG and prop/fuel line clearances. When I built my Avistar, I put an OS .50 SX on it, which is a little heavier than the typical .40-.46 sized engines spec'd for it, so I just put it as far back as possible to minimize the nose heaviness of it.

So you can either put the whole thing together and then play with the engine placement to help get the CG right, or just put it where you think it looks good (making sure you have good prop and fuel line clearances) and just use your batt placement for the CG.