I usually scatter a few around and then go back and fill in the area-it seems to work for me that way.
The texture is amazing and at present I am using DMC Perle 8 thread but I also have to use floss as well and the scattering of the knots in the beginning helps to blend the two different threads as well.
I have gone around the outer edge of the yellow knots with backstitch to give it more definition and I will do the blue when I start on those knots.

I am pleased with the way this is shaping up but I have thousands of knots to go--it's a good thing I like doing them.