First, there are some programs like the Daily Show where the channel uses exactly the same data for each showing on a single day, marking every one as first run, so the DVR does what it is told and records them. Comedy Central is notorious for doing this. Setting up a recurring manual recording as suggested by joed32 is the only real way to solve this,, other than just deleting duplicate episodes after the event.
Second, for other programs the DVR is totally dependent on the guide data. Remember though that when you first set up a series link, the DVR will record the first episode even if it is a repeat, it uses that episode as the "foundation" for the series link.
rom that point on, the DVR should only record first run unless the guide data is screwed up. But as MikeFr posted, just because the episode is in the to-do list does not mean it will get recorded. Often the episodes don't have full info at first, so the DVR sets them to record. Later the guide gets full nfo, and if the episode is not first run it will not get recorded.
Some people spend hours "managing" their to-do lists. Unless you are trying to sort out conflicts it's not worth doing that. Just let the DVR do its thing. I can count on the fingers of one hand the number of times I have looked at the to-do list this year. The only time I have missed a new episode of anything is when the showing was pre-empted, and then when it was repeated the guide had not been updated and was showing that it was an old, repeat episode.