My game runs with very low FPS

Q: Normally my game runs fine, but when launching through SkyrimTogether.exe the performance is terrible

This is most common in laptops or systems with an integrated graphics unit built into the CPU. The solution is to configure your system to use your dedicated graphics card rather than your iGPU.
There will be two options available to you. Depending on what you installed Skyrim Together Reborn with, either MO2 or VMM.