It should. It depends on how the USB device is setup. If it allows you to install EasyBCD then it should edit it no problem. If you install it on your Primary drives it will not allow you to edit the USB devices at all. You will haev to install it on the USB Device to edit those entries.
I've created two partitions on the 1gb USB flash drive (using Acronis Disk Director 10):
Partition 1 for DOS: 64mb, FAT16, primary partition, active
Partition 2 for WinPE: 909mb, NTFS, primary partition
However I can't get my Windows XP or Windows Vista workstations to recognize the second partition, it only brings up the DOS partition. Perhaps this is because it's a removable drive? I need both partitions recognized by my Windows workstation so I can copy the WinPE 2.0 (Vista) flat files to this drive. Once I get all files in place, then I can use Easy BCD to create the boot menu I need. Any ideas?