Just be extremely careful and buy extra material
It is a fairly difficult task. I applied both the stainless steel and the plastic tape as you are doing for the same reason. The painted surface will eventually get scratches if you don't. The plastic tape installation on the underside of the wing skin is easy and needs no description.
I marked the wing skin trailing edges on the flaps with the flaps in on full up position. I disconnected the flap linkage and lowered the freed flaps so that the curled leading edge was completely clear of the wing skin. I carefully pealed back one end of the adhesive cover paper and applied one end of the exposed trailing edge of the SS tape on the forward side of the wing skin coverage line. Then I progressively worked down the entire span of the flap applying only the trailing edge of the tape to the flap being extremely careful not to apply any side tension on the tape to force alignment with the wing skin coverage line - if you do the SS tape will kink and you will get a wrinkle that is not removable. Perfect natural alignment is required for a perfect job. If you try to get full chordwise adhesion at any point tension will be unevenly applied to the SS tape and again you will get wrinkles. Wrinkles cannot be removed but they can be reduced to a functional level with an icecream stick - they just look bad. After the SS tape trailing edge is completely attached I carefully smoothed spanwise segments into adhesive contact with the flap working in chordwise increments begining aft and worked my way to the leading edge of the flap skin (one spanwise segment at a time until the final one is pressed into contact along the full leading edge of the flap).
In this final installation, to restore it to the quality I had before paint, I used 3.5 inch SS tape and folded it sharply around the leading edge of the flap skin and onto the underside for a good grip (note: This is where you can get cut bad if you think you can run your fingers along the edge to press the tape in place in one long fluid motion - the fluid motion will produce significant blood flow - it is better to press each point down to achieve full contact at this edge). I also made the SS tape longer that the flap span and cut spanwise notches in the short overhang at both ends of the flaps. I folded them around the ends of the flap skins and onto weather strip adhesive on the underside of the flap skins at the inboard and outboard ends. They look great, there is no corner curl-up and the paint is totally protected.
A couple of things I learned are - 1) They are not kidding when they say the edges of the SS tape are extremely sharp (think razor blade edges - I have multiple cuts - some deep) and 2) if you lift the tape and try to reattach it something happens to the adhesive and it will never stick properly again. My painter did not cover the full moving interface with his attempt to re-apply SS tape and one had a couple of wrinkles. My own right flap SS tape application went well but the left one had to be redone four times before it was acceptable.
I hope this is helpful,
Bob Axsom