You don't use server.cfg, you use the gamemode_xxxx_server.cfg in the /cfg folder of the csgo root directory.
READ THIS - Documentation is available here -
https://developer.valvesoftware.com/...ual_server.cfg
Assuming you're using competitive game mode (gamemode 1 & gametype 1), you create the gamemode_competitive_server.cfg in the cfg folder. Add the contents of esl5on5.cfg or simply add
exec esl5on5.cfg in the gamemode_competitive_server.cfg.