I have one roommate not on the lease and one on the lease with me. I know I cannot legally kick the one on the lease out, but I believe because I have been covering her rent for 2 years that she will amicably leave if spoken to in-depth about this.

How would I give notice to these two roommates?

My question is in regards to a roommate situation in an apartment in: California

For the roommate who is not on the lease, if they have lived there less than one year you can give a 30 day written notice that their tenancy is terminated. If they have lived there for one year or more than you have to give 60 days.

As for the roommate who is on the lease, have that in-depth talk. If they still don't pay then your only option is to file a lawsuit against them for their share of the rent that you've paid.