Should be no problem.
Make sure your USB external disk has lower boot piority than the internal one, then everything should work as expected.
If i plug it while windows is running(after boot), will it mess up my current windows 7?
Not sure if you even know why two OS disks could be a hazard. If they both have the same boot signature, as would result from cloning a disk, having them connected internally might make both unbootable, and you'd have to insert the Win install CD and select the "repair" option after removing the drive you're least inclined to boot from.
I don't think that the drive signature is exposed by an external USB box. [I could be wrong .. ]
Sorry im abit confuse. Im an asian, so my engliah is not pretty well
Let me put it another way, because my English is "too good for my own good." I run my mouth through my fingers.
If you plan on replacing your OS drive with a new one, and moving the old one to an external USB enclosure, just delete the partition on the old drive and create a new partition and simple volume. If you cloned the old OS drive to the new one, most cloning software allows you to create the clone with a different drive signature, so you wouldn't have any problem with it.
And of course, if you are just making a fresh OS install to the new disk, there should be no complication at all. But I'd still recommend wiping the old drive clean, partitioning and formatting it fresh -- for the purpose of storing just data.