RcppArmadillo ships its own copy of Armadillo to avoid exactly this problem. As RcppArmadillpo is used from R, it can rely on R (and R's configuration) to get LAPACK, BLAS, etc pp. We don't need to run configure to use Armadillo from R, and so we don't do.
RcppArmadillo installs the usual R CMD INSTALL ...
way; this is tested before every release and has worked reliably.
As you say "your ultimate goal is to use Rcpp and RcppArmadillo", you are in fact done at the R CMD INSTALL ...
. You can replicate the step from source, and test the package -- all that should "just work".
The other thing to keep in mind is what the "Writing R Extensions" and "R Installation and Administration" manuals have to say about your compiler. As far is R is concerned, your g++ 4.8.* does not exist. Only the Rtools version matters, or you get into non-standard land real quick.