When i buy a gun and equip it, it goes to my secondary. I just got a bat and when i equip it, it goes to my secondary and my gun is now in my bag instead of going to primary or at least the bat going to primary. How can i put bat as primary and gun as secondary or vice-versa 

Yes. Melee and hand weapons and such goes to secondary. While Primary weapons like A.R and such goes to Primary. That's just a game logic. Unless it's possible to do in here.

There's a set way, Primaries and Secondaries are defined, Assault rifles are Primary, and Pistols are Secondaries. Thrown objects are grenades, stuns etc. Armour be armour. 

You can't mix and match these, choosing a particular weapon as a Primary and or Secondary.