I agree with Irishrose about the ruffle making the top difficult to keep neat. Here is what I would do. A single fullness of fabric for the table (i.e. the 109 inches but I'd probably give myself a couple of inches for 'fudge factor' as well as making side hems). If you want the ruffle for the 'pretty factor', go ahead and double that width for your fullness. Make the ruffle separately as you initially mention. I would sew the velcro strip to the flat skirt (making top/bottom hems beforehand). Then sew the ruffle onto the skirt with wrong side of ruffle to right side of skirt. Kind of like a 'top dressing' for the skirt. Both pieces then stick to the table together. I would put the large ruffled side towards the floor, thus having less fullness at the top edge for things to get lost in.
For me, I probably would not do any ruffle just so there was not some place for little things (pins; bobbins; etc.) to hide on me! You might want to do the 3 pieces of fabric as suggested for ease of access to your bins under the table. Maybe even an overlapping slit in the front for the same reason. Just remember to add in those extra inches for side hems on each piece of fabric.