How to position piano pedal lines precisely.

I'll answer the question in a random order that makes sense to me. I will give some additional info that might help as well.

The pedals are supposed to line up automatically in a system (a single line of music). If they don't that's a bug. If you don't want them to line up, turn of Automatic Placement in the inspector.

To fine tune a pedal's position left, right, up or down, double click the pedal, click or tab to the middle grab box and use arrows for small adjustments and ctrl + arrows for large adjustments. If select an end grab box, a red dotted line will be drawn to the note that end is attached to for playback purposes. If you want to change the anchor note, press shift+an arrow to change this.

To copy and paste pedals, it's best to copy and paste notes and everything, then change the notes, text, dynamics in those measures.

The best way to apply a pedal to start with is to select the first note, then shift+click the last note you want it applied to. There is one exception to this. If you want the pedal to cover a single note, click that note then ctrl+click the next note or rest and apply the pedal. You would of course want this if the bass, where the pedals are applied, has a dotted half note and 8th note arpeggios in the treble that you want the pedal applied for.

You may select the range the pedal covers in either the treble or the bass, but the pedal always appears below the bass.