You can index RT with is.na(ACC) like this. This answer will work if RT and ACC have the same dimension.
#example data
RT <-data.frame(matrix(1:25,ncol=5))
ACC <-data.frame(matrix(rep(1,25),ncol=5))
ACC[c(1,3,5),c(2,3,4)] <-NA
#Put NA in RT where ACC is NA
RT[is.na(ACC)] <-NA
RT
X1 X2 X3 X4 X5
1 1 NA NA NA 21
2 2 7 12 17 22
3 3 NA NA NA 23
4 4 9 14 19 24
5 5 NA NA NA 25
