Create mod presets. Select 'Mods' from the ARMA dashboard, clear all loaded mods, load the 506 mods and in the upper right hand corner create a new 'preset' with the name of your choice. Unload the mods again, load your custom set for missions other than 506 and create another preset. clear the list and load the preset depending if you are doing 506 stuff or not.
Also if you are editing missions in Eden, the save path for missions is different for each user profile you have, If you have a 506 profile,the missions folder, under the default Documents or whereever you have it may be wrong, so be sure to load the right profile for whatever you are doing.
If you are just connecting to a server ( other than 506) and it complains about mods or it punts you completly; in the ARMA dashboard, select 'servers' , select the server that punted you and select the option to load any missing mods, specific to that server.