The best position is determined by YOU and what YOU are comfortable with, with your personal technique. The rims should be low enough so you don't hit them constantly when playing.
Do you have a drum where you like the position of the crown? Then try and get the crown down to that level. Remember after you get the head on there you can lower it by tightening the lugs while still wet. Do that gently, little by little. Also remember the rim will drop when you tune it after it dries. Of course you have to drop the rim down to the level to get the lug on. A characteristic of Valjes is the rim needs to go lower than other drums because of the way the Valje lugs have that hook. I have 5 Valje congas and 3 Valje bongos, so I know what I'm talking about. So don't worry about it.
I've reheaded skins perfectly where the skin stays the same color all around, and I've supposedly "messed up" a little and the skin got a little white around the edges. Supposedly "stress" causes the white. I never noticed any difference in sound or longevity of the skin. I think it's a purely cosmetic issue and I don't stress if it happens.
Ultimately, there is no by the numbers method to describe to you. Every skin, drummer and drum is different. I've changed about 50 skins now on all sorts of bongos and congas. You just have to do it and not worry too much about it. There are all kinds of techniques written down here in congaplace, like the string method, the extra long lug method, the mixing bowl method and the wire method.
You never actually know what a skin is going to sound like until it's on your drum and you tune her up.
I wrote an article about conga skins here a while back you might find interesting
http://rumbainstruments.blogspot.com/20 ... rumba.htmlOkay, good luck.