I make all of my color separations by hand. It's a lot more fun for me that way (also, I'm not too versed in the computer department) I like to work straight onto the Vellum and I usually use a combination of pens and oil markers to ensure opaque-ness. The top image is the white separation.
After I have all the color separations ready, I can get to my favorite part which is printing! Here we have the blue and pink colors printed, which, layering the two colors on top of each other with the right transparency ratio makes purple.
It gets better! Printing the transparent yellow layer will then bring out a whole slew of other colors, with beautiful green and orange and browns.
There's an endless amount of things to keep in mind in order to ensure quality printing. For every layer to be printed there is an elaborate process to it. Before shooting your image on the light machine you have to make sure that the coat of thin emulsion on your screen is absolutely dry. I found myself still having to fix my images after each and every shooting.
Here is what the final print looks like after the white and line work. The paper I've always used is the Rives BFK cream color and I love mixing my very own brown for the final line separation, which I think goes perfectly with the cream paper.
Something to keep in mind while printing the paint through the screen with the squeegee, make sure you are printing at a 90 degree angle. I've only recently been tipped off to do this, and it was challenging (on my back!) at first, but it can prevent things like a flooded image. The paint also needs to be the right consistency, like melted ice-cream. There is seriously so much to the process!