I agree with the rest here so far. Also you can buy special feet with a 1/4 inch guide edge. That may help to keep them straight. Be sure you pin your seams to match. The fabric can stretch a bit to ease in some of the uneveness(if that's a word)if it isn't too far off. By pressing the seams in opposite directions the seams will settle in for a tight match. Also they suggest that the seams be pressed toward the darker fabric to show less.
I would embroidery first then use the template to cut you square. If they are not butting up it is because your not sewing it excatly 1/4 inch. That happened alot to me when I firt started. Use pins to meet the seems together. See if that helps. Cloey
The trick is to always start with larger squares than you want , The fabric will shrink while embroidering . Then talk your ruler and Square them up . so when you piece your quilt you start out with true squares. Good luck A shamrock for all
In mid summer of '06 I decided to bite the bullet and make quilts for my grandkids for Christmas. Not a good idea in hindsight. I had never made a quilt in my life before.I was very stressed for several months. I had 4 grands at the time and 1 on the way. I was just finishing up the last quilt for the one on the way when we found out that it was 3 on the way. So I had to make 2 more. I learned a whole lot about quilting and stress during those months. I wish you great luck. Once you learn the tricks it's not so bad. And jrob is right, don't cut your squares to the final size until after they are embroidered.
Try this: Cut your squares at least 2 1/2 inches larger than you want them to finish out. Embroider them, then trim to the size you want centering your design. I am guessing that some of your embroidery is causing the fabric to "shrink" more at some places than others, so if you cut bigger to start with then trim down to desired size you should not be crooked at all. ;)
Great answer jrob. I learned that the hard way too. I start with a 10" square to get an 8" finished block.