When I do sampler blocks I check to see if there is a generalized theme of strip widths in all of the blocks. Say you need 2 1/2, 3 1/2 and 4 1/2 blocks. I cut the fabric into these sized strips and put them in marked ziploc baggies. As I am doing a block I pull out the strip I need. Even if you do Eleanor Burn's way with flying geese I have at least a full strip of fabric cut for the correct fabric square, that way I can just cut the fabric into a square and then make my geese.
Others have cut all parts of each block and put all the pieces into a ziploc baggie then sat down and sewn the blocks. No matter how you do it there will be a challenge. One thought is to make sure you measure twice and cut once because it can be confusing when working with different blocks.
Even though they can be more time consuming and frustrating I love sampler quilts....