That's OK. The bitcoins will appear in your account the next time you open your wallet program. Bitcoins are not actually received by the software on your computer, they are added to a public master account shared by all devices on the network. If you receive bitcoins while your client is not running, when you open it later, it will download the blocks and update any transactions that have not yet been recorded, and those bitcoins will eventually appear in the wallet as if they were received in real time. You only need to use your wallet when you want to spend bitcoins.
