During the first 5 innings the pitcher is not in the line-up, has a DH. Starting pitcher leaves and the relief pitcher comes in from second base, he stays in the line up as does the DH. Sub at second never enters the line up. Sub at second makes a play in the field. How do you note this? Not in the box score, but where do you notate that a different player is at second if not in the line up so he gets credit for the assist?

If I understand you correctly you have a DH for your starting pitcher. Then you remove your starter. If so then you still have a DH but the new second baseman enters the lineup in the place of the starting pitcher but you keep you DH.

So.... your sub enters the lineup for the pitcher. If using stat software then you enter the new 2B for the starting pitcher defensively. If keeping just a book then still show the new 2B entering and the inning entered.

A short look at the line-up card looks like this:

RF - Gary
2B/P - Joe
DH - John
.....P - Dave
.....2B - Al
3B - Mike

Even if the DH never comes around to bat again.