If you submit your apps now, the schools will request your report, including LOR's, and they will receive it in its present state. Then, when your second LOR arrives, it will automatically go out to all of the schools that got your first report.
A word of warning: Some schools will let you go complete with fewer letters than you ultimately end up sending. If you expect the other letter to get there soon then this is not that big a deal, as it will let you go complete earlier but your additional LOR will probably arrive at schools before your file has been reviewed. However, if you won't be getting the letter until much later, your file may end up getting reviewed without it.