That sounds like the best idea yet! And it would not shift out of position either.
That lady at your store must have meant to use the stencil in the same way, quilting around the outside edge. Although I would make a pattern off of the stencil and preserve the integrity of the original template.
I have trouble even getting chalk marks to go away and there is now way i would try the markers after reading all the negative comments about them.

I use these templates all the time. I assume you're going to use this template more than once on your quilt. Get some Golden Threads paper, sold by the roll at your LQS. Draw the design on one piece of the paper then use your pen or pencil to fill in the broken spaces so you have the full design. Count out how many times you will use this design on your quilt. Stack up enough pieces of paper for the design. If you will use it 10 times, cut out 9 pieces. Stack them up, design on top. Staple or pin around the edges to stabilize. On your machine, use a size 16 needle, drop the feed dogs, remove thread and bobbin. Stitch around the design, thereby punching holes along the design. (You can stack up to 14-15 sheets at one time.) When finished, undo the sheets and place them on the areas of your quilt where you have planned this design. Pin sufficiently to hold the paper in place. Change your needle back down to 12 or 14, thread your machine and start stitching along the design lines you have punched in the paper (feed dogs still down). Remember to start with one stitch to pull up your bottom thread to the top, do a few tiny stitches then start your regular free motion stitches until you get back to your starting point. Once finished, simply tear off the paper. As it's slightly heavier than tissue paper it tears very easily. I keep a pair of tweezers for corners. This is also a great way to do borders. I would suggest you try a sample piece first and see how easy it is.

I see why the clerk said to snip the 'bridges' as someone called them. She meant once you do that, then you can follow the design left behind which is the same design as when left as one piece with the 'bridges. Her way, you just don't have as much template in the way. This is the same as some of the templates I have used in the past for painting and you have to remove the inner plastic to get to the outer design.

However, I think it would be better to leave together and use powdered chalk and 'pounce' it on the design, lift, move pattern to next spot, etc. or use a washable marker.

I guess it is one of those things you have to see used to understand.

I use traceing paper all the time-just trace the design and sew on the lines. I have a friend that loves to tear the paper and so I let her. I am just a beginner quilter so I have trouble with FMQ.

I do this all the time. If the pattern isn't too big I also use the scanner the make copies onto light weight paper. Both ways work great.

Maybe she thought the quilter wanted to lay the template on the top for FMQ. Not that that would really work, but in that case, the tabs would have to be out.

Somebody recently introduced us to "Frixion" pens by Pilot. You trace with them then put the hot iron on it & it disappears.

I found a pkg. of 2 at Walgreen's for $2.99. I tried one on a practice fabric & it definitely works.
I also found a pkg. of about 6-8 in colors on line & I think they were $11.99. Didn't order them though for now. Not sure I'm remembering the price right though.

You can also use Crayola washable markers. I had a quilt marked for about a year, finally finished it. Washed it and the marker came right out. Still use them. They come in all sorts of colors that make it easy to use on all colors of fabric.

The lines make it a stencil. If you cut it apart, it becomes a template. Your choice. To use it as a stencil, you can use chalk pencil (ONLY WHITE OR GREY..ask me how I know!), purple markers, or pounce chalk. When I use pounce chalk, I put a small amt in a plastic cup and dip a disposable foam brush in it. Wipe across the stencil, checking now and then to see if I have enough. I found 'pouncing' produced a cloud of chalk dust. YUCK (this was not my idea. I got it from a Kimmy Brunner DVD) Mark it as a template the same, but no chalk.