If I add extra holes for hair, I just try my best to line them up evenly. I poke the holes in the pony with a sculpting awl and then rehair as normal. Normal for me consists of inserting the awl into a hole, readying a plug, then removing the awl and inserting the rehairing tool while the hole is stretched out, then repeating the process on the next hole.
As to connecting the mane holes to bang holes, thats a personal preference. I honestly hate the gap the G4 ponies have just after their bangs, but normally I just leave it alone and cross hatch the mane.
As to dying the hair.. This was discussed a little in another thread, and the general consensus was that it would probably be best to set the dye with vinegar, as the dye instructions list. I have dyed hair while it was already rooted in the ponies head and had no nasty bleed effects. Maybe someone else can offer further advice. I haven't done black specifically.