DO NOT needlessly plug the programmer into Fusion or Pegasus (depending on your programmer platform). All it does is create issues for both parties.
You will get an email alerting you to the completion of your custom programming.
As an aside, PLEASE DO NOT use the forum to post things such as "I ordered custom tuning 'X' ago and they were done in 'Y' weeks
".
Few orders are 2-3 week ordeals and when somebody's tuning takes 2-3 weeks (or less than the advertised 4-6 weeks), then EVERYONE expects their custom tunes to only take 2-3 weeks to produce and rarely does that happen (then people get upset with the "where are my tunes" questions. Nobody is doing anyone else any favors by proclaiming that their tuning took less than the advertised time.