The tape method I am suggesting is the easiest and fastest, as well as providing the most protection against rainwater. It will take less time to install it than it will to read the lurid instructions below. Sorry for the filibuster-length post...
Here is how you would do it on an elevator:
1) Put a drop of thin penetrant oil on the hinge pins and work the elevator back and forth to make sure your pins are not stuck or galling.
2) Clean the elevator and stabilizer surface with rubbing alcohol to remove any dirt, grease, oil, etc.
3) Using a small "acid brush", put a very thin coat of vaseline over the top surfaces of the actual hinge tubes (both the elevator and stabilizer hinge sections).
4) Move the elevator into the full down position (stick forward). Put a weight on it or bungee the stick forward all the way.
5) Apply the 2 inch wide Blenderm centered halfway on the elevator and halfway on the stabilizer. As you apply the Blenderm, use your little finger to push the Blenderm down into the gap, as opposed to stretching the tape taut over the gap. You do NOT want the tape stretched taut, because it could restrict elevator movement. (So to answer your question directly, the Blenderm does not go from top to bottom or bottom to top, it's on the top of both stab and elevator.)
6) Burnish the tape down (and down into the gap) using your fingers. Burnish it down until the tape turns the same color as the paint, meaning it is all stuck down good.
7)Verify that the Blenderm does not "shear" because it stuck to the two parts of the chinge that move relative to each other.
8 ) Verify that the tape does not get so taut that it tries to prevent the elevator from reaching the full "down" position. Verify you have full, free, unrestricted movement with no resistance, rough spots, etc.
9) if you wish, bungee the stick fully back (up elevator) and do the bottom of the gap the same way. If you choose to do the bottom, attempt to stick the two layers of Blenderm together in the middle of the gap if you can. This is absolutely NOT necessary but it will serve to prevent an ugly strip of dirt from sticking to the underside of the upper tape.
10) On an annual inspection or every few pre-flights if you like, check to make sure the tape is not ripped, and not "shearing" where the hinge sections move relative to each other.
BTW the only way you can do this on an aileron is if you have the same type hinge (welded tube hinge or piano hinge) as you have on an elevator. But the standard "Frise" type aileron hinge method (offset hinge, as seen on Taylorcraft, Cub, etc.) will not allow this type of tape seal. For that, we have to use a different seal called a "wiper seal", which has its own quirks and procedures to work correctly... but alas, that is the subject of next semester's course in control and gap seals

Since this thread is about VG's and gap seals, be aware that you may still need VG's on the bottom of your stabilizer to get the maximum control authority (to match the extra AOA capability that your wing VG's give you). That's not a bad thing, but it certainly will give you more elevator power, which like all power, can be abused. With VG's on the bottom of your stabilizer you will be able to exert more elevator power, meaning more wing bending loads. Please check with the Ridge Runner's designer to make sure you have the structural reserve for this. Your life genuinely does depend on it.