Assembly of PCBs containing a mix of SMT and thru-hole parts?
Both approaches are valid.

Hand assembly would require that the paste mask for the SMT devices prevents putting any paste on the thru-hole pads at all. Then you use wire solder as usual during the hand assembly phase.

Thru-hole devices can be soldered in the reflow oven; this requires a technique called "paste-in-hole" &mdash; but it doesn't work with all components, and the PCB has to be designed for this from the start.