Via in pad is that the via holes in the SMD pad, it is not good at PCB assembly process.
General, there are 3 methods to solver it.
1. The Via is 0.3 – 0.6mm, and solder pad is big ( >5times of Via holes ) ,
Could use solder mask filled, it is economical.
2. Via is small and the solder pad is small （ Via in BGA )
Could choose Via filled by resin and plated over or plated over by copper directly.
For more detail , please check follow