Are your designs specific for quilting on an EMB machine or are they general designs that you are using to make quilt blocks.
Specific quilt designs will have the placement and tack down stitches built in for the design.
General EMB designs won't have these steps.
I hoop a piece of no-show-mesh first. Add and set the design into your machine.
In most designs, the first stitch is placement stitch. Cut batting about 1/2 inch larger and place over the line. Then stitch the "tack-down" stitch for batting. Trim around batting close to stitch line. This step prevents bulk from batting in the seam lines later.
Check the steps in the design and it should have a Second placement and tack down for the background fabric. You want the background fabric larger by at least 1/2 as this will be the seam allowance in quilted EMB blocks.
Stitch out the EMB design and or applique on the quilt block. When finished remove from hoop. Trim outside of the tack down outline by 1/2 inch. I use a large ruler and square up at the same time.
You can trim out the no-show mesh against the tack down line (from back of block) to eliminate bulk.
This method works for me as there is no batting and background fabric layered in the hoop.
Remember if the EMB is more than 8000 stitches it needs an extra layer of stabilizer to prevent puckers. Tear away works well. Just lay it carefully under the hoop and let the stitching catch it. No need to hoop it with the NSM (no-show-mesh).
PS: There might be a tutorial in the design pack to show how to quilt blocks.
Good luck!