The title commitment lays out the blueprint for the title policies. Marking it up indicates to the preparer of the policies that you have completed conditional items and how they should adjust the exceptions for the policies.
For instance, Schedule B1 might say that you will subordinate a mortgage. By marking that item as "complied with" you are telling the file and anyone that needs to know, that you took care of it so they don't have to.
On Schedule B2, let's say you have an exception for restrictive covenants and the mortgage lender wants an endorsement covering any violations of covenants. You mark - or handwrite a note - on the Schedule B2 indicating which endorsement will be issued to cover that item in the loan policy.
So, basically, it's a record that you did your job and an instruction sheet for whoever will produce the policy.