I plan on using a USB 3.0 Motherboard in a 2.0 Case, I know I won't be able to use 3.0 in the front, And Im ok with that. Is it compatible?
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Can you link the Motherboard and the Case you plan on using?
Also you can install the 3.0 panel in the back of your Cabinet.
The jacks in the front panel aren't usually ever used by most people except for the occasional usb device but you could use an extension lead from the back for that purpose. You could just not connect the front panel jacks, that would solve everything.
As long as the motherboard panel jacks fit properly into the case panel gap, you are good to go.