I run a linux server but I think this applies to a windows server. At the following line to you command line:

+mapchangecfgfile "server.cfg"

This will cause the server.cfg file to be read with each map change. The max-min bots command does not function fully this way as bots will not add back in after players leave. If anyone has a work around for this please post.
Here is my command line:

./hlds_run -game cstrike +ip 69.93.97.59 -port 27015 +mapchangecfgfile "server.cfg" +maxplayers 24 +map de_aztec

Hope this helps

Cooley