if your structure is:
-maps
map1lol.bsp
map2lol.bsp
-beta
lolmap_b1.bsp
-hax
omfghax.bsp
then you would do 'map map1lol' to get to map1lol.bsp, of course. 'map beta/lolmap_b1' to get to lolmap_b1, etc.
However, if you join a server, your client-side copy of the map will have to be in the same place as the server's.