No, you are confused.
Say you download a map (ns_siege007.bsp for example) from another server and you want to play this map with bots on your own server. The map is to stay where it is and does not need to be replaced unless it was corupted or incomplete.
What you should do now is visit
RCbot home page and click the waypoints link or visit the
RCbot waypoints for NS board in this forum. If for some reason, you still can't find the waypoints your looking for then start a new thread in the
RCbot waypoints board requesting waypoints for the map in question and if possable, a link to where we can also get this map.
All RCbot waypoints for RCbot 1.0 and above will go in the half-life/rcbot/waypoints/<mod of choice> folder, NOT in your ns/maps folder.