I add enough to the baluster's overall length so that the base will penetrate the tread by about 3/4 inch when the top is fully inserted into the handrail, and use a piece of masking tape wrapped around the base to help indicate my cut line.
There are often burrs and rough edges on the baluster base after the cut, so I clean them up using the side of the spinning cutoff blade.
Both epoxy and construction adhesive tend to get everywhere, so I wrap the base and top of each baluster with masking tape before installation to make clean-up easier.
Since the stair parts usually have their final finish when it's time to assemble the balustrade, I retape the drilled treads and mask off the underside of the handrail.
I insert all of the precut balusters into the treads without any epoxy, fit the tops into the glued handrail holes.
I lift each baluster up fully into its handrail hole, slide the shoe up away from the base, and inject the two smaller holes at the base of each baluster with enough epoxy to completely fill them.
To keep the balusters from sliding back down into the tread holes, I fix each one in place with a spring clamp while the epoxy sets up.
When the epoxy is partially cured but not fully hardened, I carefully remove the protective masking tape from the treads, handrail, and balusters.