In general, multiple at5 maps are fine but just be aware that RM always generates using the default name (large.at5), so you will need to change that to prevent overwriting the first map with subsequent ones. Also, as mentioned before, things get a little tricky with multiple maps over raster, especially if transparency is involved. There are ways to do it, but it takes a bit more work (export sets of shapefiles, plus the required raster files, and generate everything together in the IMC).