-- Last Updated: Sep-29-12 1:02 PM EST --
going out with it using a pack (filled with something light) as a straddle bag. Just fill a garbage bag with styro peanuts or rags or whatever, double bag it, put it in the pack and kneel straddling it - the Becky Mason trick.
Then go out and find the bag placement where when you kneel straddling the bag the water gathers in puddles (you did remember to track some in on your feet, right?) around your knees to perhaps under your butt. The puddle should settle in about the same place fore and aft as where a sculling draw or pry moves the boat straight sideways without a change of heading.
Mark you butt position with a grease pencil and put the front of the new seat or your kneeling thwart there. (BTW, If you decide to make a kneeling thwart, make it a wide one, maybe 3 or 4 inches, like Bell's used to be. Tilt it forward. A narrow untilted kneeling thwart can become an instrument of torture at the end of a long day.)
Then move the portage yoke as (and if) necessary to allow you an easy exit without risk of foot entrapment in case of a swim. If it doesn't balance properly on the yoke, do as previously suggested - carry a paddle or strap your throw bag on something to bring it into balance for carrying.
Or you could just put a kneeling thwart in where the regular thwart now resides (as Nova Craft does, for instance. I think they place the thwarts for optimal hull strength, not paddling trim)and ballast as necessary with water bottles or camping stuff to get the trim right. Different boats require differing weights to trim. My Prospector needs quite a lot of weight to trim, but perhaps the Penobscot has less rocker and might require less ballast.
BTW, colors should be getting pretty good on the Kickapoo about now. Might want to do your trim experiments there... plenty of chances to see how she turns when heeled. :-)