I use a batch file (.bat). It launches ARMA with specific mods only. Save this modline (for Windows 7 64 bit) in notepad as a ".bat" file.
"C:\Program Files (x86)\Steam\steamapps\common\Arma 3\arma3.exe" -mod=@CBA_A3;@sthud;@st_stamina_bar;@RHSUSF;@RHSAFRF;@task_force_radio;@506th;@AllInArmaTerrainPack;@ACE
Once saved, double-click the icon and it launches default 506th mods every time.