I used a flat white Dbrand skin and put my stickers on top. My stickers have 100% coverage: https://twitter.com/rxcs/status/888214143097987072. No problems after 2 years aside from some slight fading of the colors on the reflective stickers.
If OP is in this thread, check out 3M 1080 (or newer) series. It is used on cars, designed to not bubble or leave residue, and comes in clear.
3M 1080 is great stuff - I avoided clear vinyls however as i found they lost the metallic look due to them being a little too glossy, even with the matte ones.
The Apple logo is recessed enough that I could trace it easily with an x-acto knife. The stickers I used didn't stick to it very well, interestingly, and just peeled right off.
If OP is in this thread, check out 3M 1080 (or newer) series. It is used on cars, designed to not bubble or leave residue, and comes in clear.