Live in MD but work in VA

I am moving to Maryland but will commute to VA each day for work. I understand these 2 states have a reciprocity agreement, and that I will pay MD income tax instead of VA income tax. My employer is telling me that I can update line 3 of my VA-4 to show that I am not subject to VA withholding, but that they (my employer) does not have the ability to deduct MD taxes from my paychecks. I am not sure what to do. How can I ensure that I am paying the correct taxes to MD?