I would definitely make two quilts! It will save you a lot of grief, plus I think they really are two gorgeous quilts rather than one quilt top and one backing.
Of all the markers out there, the only one I would even bother to test would be Crayola Ultraclean Washable markers like these:
http://www.amazon.com/Crayola-Ultrac...dp/B00IYDM814/ . You would need to thoroughly test whatever color you want to use on every fabric you want to use it on. I would use scraps of the actual fabrics, iron over the marks, set them in sunlight for a day, then wash to see if every trace comes out. Also, I would Google these markers and see if anyone has posted difficulties with getting a color out of their quilt.
I would not try to use any kind of colored chalk or the Frixion pens. The dyes in chalk are notorious for not coming out of fabric, and the Frixion pens can leave permanent shadows on some fabrics.
Depending on how you decide to quilt, you might want to consider using freezer paper templates ironed to the quilt top for FMQ. If you have an Accuquilt Go! cutter, you might even be able to find a die for a design; this makes it super easy to cut out a lof of templates in a short period of time. I also recommending investing in the Jenkins freezer paper; much easier to use in the die cutter than regular freezer paper because it is already cut into flat pieces (it is also thicker than regular freezer paper). Here is a link to the sheets I like on Amazon, although you can also get them from the Jenkins website:
http://www.amazon.com/C-Jenkins-Free...dp/B00114Q5NU/
The templates can be peeled off and re-used too.
If you cannot find a die to use for the freezer paper templates, you can draw your own. A quick way to cut them out is to cut over-sized pieces of freezer paper and trace the design onto one piece. Layer that piece on top of up to 5 additional oversized pieces. Iron around the outside edges so they all stick together. Use a good pair of scissors to cut around the design and, when you are done, you have 6 templates from 1 tracing and 1 cutting.