How to Apply Window Functions in Frequency Domain?
You need to use the Convolution Theorem.

Namely, when you want to apply an LPF Kernel in one domain (Using convolution) you can use multiplication in the other domain.

The tricky part is the dimensions of the signals (Since we're dealing with Discrete signals).
Since the LPF Kernel in the convolution domain might be different then the size of the signal it is applied to, so how do we multiply?

Well, the solution is given by interpolation to the correct dimension.
This is done by adding zeros at the end of the signals.
Pay attention that the end of the signal in the frequency domain is tricky.
The end are the samples before the sampling frequency (On both sides as it is symmetric), add zeros and keep the signal symmetric (If you signals are real in the other domain).