I print out a paper composite copy of my design. Place it on the platen (I also use center lines on the platen) align and square it with a T-square and tape sides to hold in place on the platen. I place scotch tape on the backside 4 edges of each transparancy. Carefully align each transparancy one at a time on the composite. Place a screen on the print head, secure and drop down on the platen. Rub edges of the transparancy to secure taped edges to the bottom of the screen. Remove screen and burn. Repeat for each color. After screens are washed out and dry, place on print head clamps, drop down onto the platen with the composite. Visually align with the composite print and secure the clamps. Repeat for each screen.
Some minor adjustments are usually required, but always minor.
This might not work for you, but I've found it to be the best and easiest for me. Good luck.