First dive on EAN 36 is conducted using EAN 36 tables. After the surface interval, you take that letter group designation and switch to the EAN 32 tables to get your RNT for the second dive using EAN 32. The residual nitrogen is nitrogen already in your body before you start the dive on EAN 32. It is as if you've already dived at your planed depth for the residual nitrogen time on your next mix.
One note of caution, while you do switch tables, you must stay with the same type table. If you start with the PADI EAN 36 RDP, you switch to the PADI EAN 32 RDP. You must not switch to the US Navy tables, the SEI tables or any other table. Of course, the same applies if you start with the US Navy tables (or any other), stay with the US Navy tables (or which ever you started with). An A on one is not an A on another.