Got the losi 2109 exotek diff housing and it says I can use it with stock internals but it’s not the same internally at all? Stock uses square pieces and square notches in the case to hold your spider gears and the Exotek one has weird half heart shaped designs in the case? Do the squares perfect slot into those shapes? Or do I drop the square pieces all together?

You might have better luck asking this question in a model-specific thread. I assume this is for a Tenacity/Lasernut? The stock crosspins should drop right in.

If it's for a TLR, sounds like a G1 diff case and not the newer G2 style, completely different internals.