We've had an IR for longer than Yahoo has had formal IR spots, so we use the same rules we've always used.
You can place a player on IR once he is listed as Out. And we never made that limited to an official Yahoo/NFL 'O' designation (because sometimes Yahoo is slow to change the status)--if the team announces he's not playing due to injury, you can designate as IR. And you can keep him on IR until he plays again. Once he plays, you have until his next game to add him back to your team. If you don't add him back after that week, you have dropped him.
So, guy is listed as out for week 4. As soon as they announce it, you put him on IR. If he plays in week 5, you have until his week 6 game to add him back to your squad (unless he gets listed as Out again in that time frame, restarting the sequence). If you don't add him before week 6, he's dropped and anyone can submit a waiver claim for him.
Before Yahoo made IR spots part of their system, we would just drop the player and note in an IR message thread that he was on IR.
So all of that to answer the question. Now with official IR spots, Yahoo still only allows a player to be in that spot if he's 'Out'. We've kept our same rule though. So we can use the IR slot much of the time, but we still sometimes end up dropping the player and notifying the league that he's officially on your IR (because he still hasn't played yet, but he's officially 'Questionable'--Hogan is on my IR but dropped and visible in the free agent pool for that very reason).
It occasionally leads to someone erroneously adding a player who was on someone else's IR. Maybe once a season (this season was the first time it was me...doh). When that happens, as soon as I'm alerted I reverse the transaction and notify the offending owner (just so he can make other changes and knows it happened, there's no penalty). If you burned a waiver priority, the transaction still gets reversed but we leave the new waiver ranking the way it is. It's too difficult to reverse when multiple teams were making claims, and so we just shrug our shoulders about that and say "welp, that's why you should check the IR list"