The D54250WYK you have is probably the kit version (based on the model you mentioned) and it is very difficult to plug and accommodate an USB cable using the internal USB header and route it externally. The chassis that comes with this kit is not designed for this purpose.
There are some other third party options in the market that are oriented to customers that purchased the board (D54250WYB) and not the kit, that could enable the use of the internal USB header.
See for instance the following chassis: http://www.mitxpc.com/proddetail.php?prod=3219B65W
I hope this helps,