For what it's worth, I've tried both Eigen and Armadillo. Below is a brief evaluation.
Eigen Advantages: 1. Completely self-contained -- no dependence on external BLAS or LAPACK. 2. Documentation decent. 3. Purportedly fast, although I haven't put it to the test.
Disadvantage: The QR algorithm returns just a single matrix, with the R matrix embedded in the upper triangle. No idea where the rest of the matrix comes from, and no Q matrix can be accessed.
Armadillo Advantages: 1. Wide range of decompositions and other functions (including QR). 2. Reasonably fast (uses expression templates), but again, I haven't really pushed it to high dimensions.
Disadvantages: 1. Depends on external BLAS and/or LAPACK for matrix decompositions. 2. Documentation is lacking IMHO (including the specifics wrt LAPACK, other than changing a #define statement).
Would be nice if an open source library were available that is self-contained and straightforward to use. I have run into this same issue for 10 years, and it gets frustrating. At one point, I used GSL for C and wrote C++ wrappers around it, but with modern C++ -- especially using the advantages of expression templates -- we shouldn't have to mess with C in the 21st century. Just my tuppencehapenny.