In my project I chose to use the comb linkage for efficiency. 
By only selecting pea comb birds it's improbable to get non-blue egg gene offspring. 
If a hen has a broken link it will show up at pol, and if a roo is suspect DNA testing would help sort it out. 
I intend to use the DNA testing further down the road to confirm homozygosity.
What seems to me more challenging is to keep Fibro in a project while performing multiple crosses. 
I ended up with one, just one, keeper hen from my fibro mixes. She's great, but I had a white skinned roo, and then a barred roo, and neither will produce fibro. So her breeding has been on hold. Now that a slate roo has finally grown out, the fibro hen is on an egg laying break. lol  
With crossing to marans, if barred, that would present the same problem. A barred hens sons will be barred and not show Fibro. 
Anyway, for a multiple cross project, I decided on keeping a few lines, or "pens" (although currently juggling it in one flock with alternate roo timing now that things are more progressed). But at the start I had it set up with one-way crosses of everything, and then bred the siblings together or back to a parent to cement some of those genes before bringing them to the next mix. 
So out of 7 breeds I now have 3 lines, soon to be 2.  I envision it as an upside down pyramid, or a weaving project. Just trying to first get all the desired genes into this soup, and then later strain the soup to remove everything undesirable. Although a lot was easy to get rid of early on, other stuff can pop up as you go along.