Mr. Underwood tells Atticus that he had him covered the whole time, meaning he had a gun pointed at the mob in case they got out of control.
Mr. Underwood was looking out for Atticus. His comments later demonstrated that he was not a racist, because he did not feel it was humane to shoot a cripple, but he was also just protecting Atticus.
Mr. Underwood and a double-barreled shotgun were leaning out his window above The Maycomb Tribune office. (ch 15)
Since the men had sent Heck Tate off on a snipe hunt to get him out of the way, Atticus would have been left unprotected. It seems that he did not know that Mr. Underwood was there.
If trouble had happened, Mr. Underwood could have fired a warning shot, and chances are the men would have run away.
Mr. Underwood’s involvement is foreshadowed earlier when his offices are described. The detail that he lives there is important. It shows that he would be there late at night. Atticus might have expected him, but either way he was there looking out for Atticus.