It can take a while for payments to register in that system. First the IRS (and state) accept your return. Then later they (each) actually process it. Acceptance tells you that it's in the IRS (and state) system. If you gave the IRS bank information on your return through TT, TT does not actually touch that money. The IRS grabs it when they process your return.
Before it shows up in the IRS system online, it should show up in your bank statements online and eventually on paper. It should show that the IRS/US treasury grabbed the money. That is your proof if the IRS later writes you and says that they didn't get the money, which they won't, as the same computers do both ;-). Well, what am I saying, I suppose anything is possible, but this is not something to worry about in my opinion :-). The same should apply to your state, except it should say CO department of revenue or whatever your state tax collecting authority is called.
