I thought people who are succeeding at making ideal loops might share their strategies here.
Rama instead of cutpoints
I have never tried making ideal loops appear on a protein that has already been built and wiggled - I make the ideal loops at the beginning by using the rama map to bend the straight protein into shape (instead of using cutpoints). I set the loop segments to glycine, aparagine or aspartate, then get the sheets and helices pretty close to each other by using the rama map on the loops (and often on one sheet or helix segment next to the loop). Then I freeze any long straight portion that I haven't folded yet, freeze the sheets and helices, and use bands to pull the structures into line. Once all the structures have been placed I move on to unfrozen wiggles, mutate, additional bands to increase the core, and scripts.
If you have an ideal loop and want it to stay, be sure to set the AAs before wiggling to something where each rama dot is in a good place for that AA - if a rama dot is in the green, set that AA to glycine, or to asparagine or aspartate if the dot is in the upper left portion of the green area. If you leave it as isoleucine or something else without a good green area on the map, wiggle will try hard to pull it out of the green shape.
TomTaylor tells me that he and others on his team don't use the rama map but are still able to make ideal loops, so there are multiple paths to success. Be sure to follow the "ideal protein design" rules about which way to turn your sheets and helices if you want to be able to add ideal loops later. If your sheets are turned the wrong way, or your helix is on the wrong side of the sheet, an ideal loop will not be able to form.
article on ideal design rules (only need to read figures 1 and 2 and their captions): http://www.nature.com/nature/journal/v491/n7423/full/nature11600.html
video on ideal design rules: https://www.youtube.com/watch?v=uXrQ2VWsPJ0