OK, so I don't know if this is a common practice or not.. but I thought I would throw this out there.
By my 5th CNC project I was learning the basics of 2 sided machining. On the 6th project it was nested 2 sided machining. The one thing I caught onto real fast was keeping my pins as far away as all possible. So .002" error spread over 48" is less noticeable then .002" over 12". Anyway, I don't work with anything less than 24X48 and 4 pins.
Not every project fully uses the 24 x 48 sheet just because of the size of the part. So there is plenty that is left behind some times. So having a fixed pin location payed off. I had a small bunch of parts that I had to make. Once they were done I just copied and pasted them onto the last nested project I did. All the old vectors are there so it was just a case of fit in as many parts as I could. Pin the old scrap to the table and start cutting.