as gamblor said, use tweezers, they're available cheap($1-2) at any chinese shops, get a straight and a curved one, try applying stickers one side firstthen position it slowly as you go, then when you have it mostly correctly in place, thats the time you pat it down completely. Or you could do as roller suggested. 
Actually for old farts like me, there is a certain joy and feeling of accomplishment in applying the stickers. Not to mention nostalgia kicks in making the whole experience of sticker application on TFs an enjoyable moment. Don't get me wrong , Ive had bad moments in sticking these as well but you don't have to get new toys , just get reprolabels and correct the application.
Wanted AM partner Vanguard, Myclones Dirge, G1 Victory Leo, e-hobby Dark scream ( the black version), e-hobby Magnificus
Parts- AM partner Basher-side guns, G1 Actionmaster Elite Windmill's blades[I][B]