Habitats have to be made with barriers with a habitat gate - that’s what defines them in the game as a habitat. You can, however, use the null (- has a sort of blue glow in the menu but is invisible once placed) you can then use build pieces to keep the animals in - you ALWAYS need a habitat gate though and an area surrounded by barriers. Outside of habitats staff will follow paths even through walls etc. and paths can be placed under floors if you want.
I’m still not really sure what you’re trying to do - I don’t know what you mean when you say that paths don’t go into buildings with a floor base, for example.
I’d recommend looking online for some basic tutorials, or just looking at the buildings and habitats in the scenarios to see how they work and run through the scenarios if you haven’t as they form a kind’ve tutorial.