Ok mate, since no-one else wants to rise to this question. I will simply tell you what i do, and let you make a decision on your own heh.
For starters i always spray black. When spraying black you can never accidentally leave an embaressing spot white simply because something like the paint bubbled over it and then burst when drying. Black makes sure that even if you dont do an amazing job it wont look like you have missed bits.... so much.
Scales i will generally paint each scale individually your base colour, being careful not to get in the gaps. To me its more important that i dont fill in the gaps than going right to the edge. Then proceed to either highlight each scale individually or drybrush over, either way you cover over any spots which you didnt quite get close enough to the edge of the scale with. Generally to make my scales pop a bit more, i will add an little extra highlight to the scales at the edge of a group of them, either by highlighting the ones in the highest position, or simply drybrushing all the ones at the edge towards the middle. And as long as you have not gone over the edges with your basecolour, this will leave it black(or the base colour of whatever flesh your doing) where the scale meets flesh, and then straight to a fairly light colour making them really stand out.
Personally i normally highlight each scale individually, as you will end up with a much cleaner looking model. But if you dont trust your own hand to do that, drybrushing works just as well.
As for muscle tone, i am not sure what you mean. Do you mean colour choice or muscle painting technique?
Again dont take what i say as professional advice. Its just what i do and it works for me