The method that has worked best for me over the years is to use a steaming hot tissue or cloth pressed over the decal once it is positioned. I use a small elctric pot to keep close to boiling water, then dip the cloth and damp off the excess water on a paper towel and then press the decal. It will conform and lay down instantly with no wrinkles. Do not hold against for more than a second or two or it may cause some damage to the surface layer of the decal. A Q-tip can used for smaller areas. This works on any brand of decal without fail. Also you can use hair dryer on the lowest setting, making sure to keep it moving and not overheat the model. I needed this method allot on cars like the JAACS Accord, I couldn't have done it without it. As for clear I only use Future on my models with some Zymol brand wax over that. For info on using Future check this link
http://www.swannysmodels.com/TheCompleteFuture.html
It's the safest clear coat there is. It can be removed with ammonia(which will not touch any paints except Tamiya Acrylics). I have learned to carefully wipe it on.