You simply submit your transcript when you are applying usually during your first semester senior year. The courses and grades that you have taken from freshman to your junior years are what graduate admissions will base their decisions on. Keep in mind that they will be able to see the current courses that you are taking in your first semester senior year.
Most programs I applied to (other than one which had its deadline in early Demember...because nobody's busy with finals right then
) required transcripts that had your grades from fall semester, senior year on them. Generally whoever handles transcript requests at your school will have an option, after you put the order in, to wait to mail it until after they have grades recorded.