We wish you much hatzlacha with the transfer, and may you find yourself in a healthy pregnancy soon!
It is permissible to dispose of excess semen, eggs, and embryos.
If necessary, the embryo transfer may be performed while you are niddah. The transfer does not render you niddah if it takes place when you are tehorah.
Please see our page on Fertility Treatment for a more detailed halachic discussion of these and related issues.
You may be interested in a free consultation with a Yoetzet Halacha Fertility Counselor for further guidance; please click here for more information.