You can only run the digital loop or the analog loop.  While they can both be connected at the same time, the digital will override the analog when turned on.  From the manaual...

A setting of LOOP is used when you wish to connect to an external effect processor

digitally. In this mode, the Digital inputs and outputs replace the analog effects loop on

the rear panel.

One word of caution on the digital loop.  the signal comes back to the amp L/R reversed.  Seriously!  This has been a bug since the VDI was released.  I am not going to beat the dead horse (well maybe a little ) , but I am the one that discovered it and reported it to the customer service manager however many years ago that was.  He didn't beleive me until he tried it while I was on the phone with him.  A fix was promised, but along with the other bugs that remain the L/R digital loop bug fix was abanded when Line 6 announced no further updates for the Vetta.  I know it sounds rediculous, but...  I have a G-Major so this is 1st hand experience.  If you want to test it, just use an RCA cable in the S/PDIF loop and listen to what happens.  Again, Line 6 already confirmed this as a bug to me.  The only possible workaround is to reverse wire your speakers and reverse program any effects that come AFTER the loop in the effects chain (thanks but NO) while always leaving the loop "on" (even when disabled at the effectes processor level).

Chris