My best advice, and the only method I've tried, with success, is to purchase Anita Goodesign quilt sets. They stitch out beautifully and there are perfect instructions on how to stabilize with minimum thickness. Have fun.

So much depends on the design. If I make individual blocks I cut them bigger then the final size that I need and square up after the embroidery has been done

I agree with crafter. I think people cut the squares too small in the beginning - trying to save on fabric and that is where they strike problems.

I might not be understanding your problem, but I would baste everything before I do any embroidery. I always use WSS on 99% of my embroidery with no problems.
I hope this might help you.

I always cut my blocks larger than they will finish at and like Angie, square them up after they are embroidered...If you have software, you can add alignment marks (last thing you stitch) in the first hooping and alignment marks (first thing to stitch) in the second hooping. It will help you align the second hooping with the first and the needle drops should be exactly the same when you stitch the second hooping alignment marks...hope this makes sense...Unless you have a BabyLock or Brother with the camera scanner....than it is easy peasy!

I have found that I do better without using the stabilizer if I have the quilt sandwich (quilt block-batting-backing). There is a stabilizer especially for quilt in the hoop on the market that combines batting and stabilizer, something like Battilizer?? It is from Hoop Sisters.

One more thought - use washaway stabilizer. It is thin and sturdy and will leave you with a softer quilt when you are finished and wash it.