Macbook not loading external drives on start up

I have two external hard drives attached to my MacBook Pro (running Lion) using a powered USB hub. What is the best procedure to use when shutting down the computer at the end of the night, and when turning it on the next morning. I didn't turn the computer off much when I used Snow Leopard so I can't really say that it has something to do with Lion, but I'm using Lion now and I am shutting down every night. Every morning when I turn the computer on the external hard drives don't load. I have to disconnect all the wires from the hub then first reconnect the hub to the computer, next the power to the hub, then the hard drives one at a time as they load. I would like to turn the computer on and have the external hard drives load automatically. Any help would be much appreciated. Thanks!

I only shut-down completely when I'm transporting my MBP in my backpack. Otherwise, I sleep, or do the occasional restart. I would just let your computer sleep at night and see if that solves the problem.
Regards,
Clinton

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