I did a stained glass quilt (got the pattern from a stained glass website...asked for permission & she now has a pic on her site).
Not sure what your pattern looks like...I had just a picture to go by...had to enlarge the pieces and decide colors, etc. What I did was Draw out the pattern full size on freezer paper I pasted a snippet of fabric to each section, using the picture as my guide... Next, I marked the pattern with a number and letter. Red batik was A1, A2, etc. There was 32 colors needed...so some ended up AA1, AA2, etc. I then traced all the lines with a sharpie...turned the paper over and put on my glass top coffee table with a light underneath the table. I then traced all of the lines onto fusible (note that if the design is symmetrical, you don't have to trace reversed). I then cut out the pieces and put into a baggie marked with their letters...all the A's in one bag, all the B's in one bag. I then put the original on my ironing surface and ironed it to keep it in place. Then I laid the foundation fabric over that and used blue painter's tape to hold it in place...Fused all the A's first, then the B's, etc. This worked for me, since I was using black bias tape as the "leading." I think there is a pic on this group somewhere of the cross quilt...has my little dog (shizu mix) sitting on the quilt.
There is probably an easier way, but it was my first stained glass quilt & since the pattern had tons of small pieces...and was meant to be cut from glass and leaded... this worked for me.
If I had it to do over again..I'd probably use a black foundation, and leave a small space between the pieces...letting the foundation be my leading.