No that's not what you're supposed to do. The mission.sqf goes in your server PBO, and replaces the existing mission.sqf that is in your server PBO already. You aren't adding something that isn't there. You aren't replacing your mission.sqm in your mission PBO.This is what I did;
I placed the mission.sqf in the root of my mission folder with the server_traders.sqf from the downloaded PBO. I restarted my server but the default trader cities remained.
ServerPBO > missions > DayZ_Epoch_11.Chernarus > mission.sqf
Mission PBO > server_traders.sqf
Open your Mission PBO > mission.sqm > markers > add the marker like he says and change the total number of markers at the top. Remember the markers start at zero so if you add marker #14 you really have 15.
Also I hate to sound like a dick but this was explained earlier in the thread when I was having the same problem you are.