Keeping Quads = 2 materials?

Okay so I recently made a building in blender and I made it in 4 different parts so I can easily UV map and texture it and then join it after i did it all. Now when i ticked the option of keeping quads since I like my buildings looking as squared as possible & I know Unity triangulates everything on import, So this is what I get

With quads off it looks regular

Now I will say I am a bit confused since my textures got messed up and I thought Unity would automatically detect any Joined UV's from blender. I'm not sure what order I have to place my textures after I make materials since the buildings geometry keeps disappearing. I'm really confused and if someone can give me some tips or even a thread that posted this problem before i'd be grateful. Thank you guys!