you don't have to do that.
you only put waypoints in where you want bots to be able to go. not everywhere. the automated connection routine takes care of mostly that when you save your bot file.
general rules of thumb:
1) always put a waypoint near spawn points so that your bots can pick up their path when they respawn.
2) Remember that bots follow their waypoints in numeric order and will cut paths to get to a place it needs to go to in order to achieve it's goals faster.
Example: A bot is at waypoint 30 and needs to get to a powerup in the next room that is at waypoint 90. If the bot had to follow the waypoints in strict numeric order it would have to go all the way around to get there. This is not the case. If the bot needs to get to Waypoint 90 and the onlly waypoints in between waypoint 30 and waypoint 90 are waypoints 100 - 91 and then bot will cut to those waypoints to achieve it's goals.
Bot routing is very easy to do for simple maps... but for maps with lifts and jump points it's hell.
Just be sure to place any do not enter brushes around any pits or holes you may have that you don't want bots to randomly walk into(because they will if they have to take evasive action). The Do Not Enter brushes should only be as high as a bot's feet and should be as long as the pit's length (this way the bot won't walk off and you can still push them off if you feel like it
I suggest another bot tut:
Their bot route tut was the first published and should be read by every mp mapper.