You can also try an xxxx.auto.rsc file:
“Since RouterOS v3rc it is possible to automatically execute scripts - your script file has to be called anything.auto.rsc - once this file is uploaded with FTP to the router, it will automatically be executed, just like with the Import command.”
Source: http://wiki.mikrotik.com/wiki/Manual:Configuration_Management
To upload file you can use /tool fetch command, example:
[admin@mt-test] /tool> fetch address=192.168.88.2 src-path=conf.rsc user=admin mode=ftp password=123 dst-path=123.auto.rsc upload=yes
Source: http://wiki.mikrotik.com/wiki/Manual:Tools/Fetch
But, be aware of some bugs: http://forum.mikrotik.com/t/fetch-upload-auto-rsc-between-routers-not-executing/56819/1