Hello Guillaume,

you can implement QoS on two parallel L3 links (I suppose each line has its own ip address) exactly as if the line was only one.

You need to assign to both links the same resources taking in account that if one link fails all Voip packets need to go on the still alive link.

if VoIP traffic flows have different source and destination addresses there are chances both links will be used (not a perfect load balancing)

I suppose you are using default per destination load-sharing that with CEF becomes a combination of source and destination (logical exor)

you can use a LLQ (priority command in policy-map) for VoIP

you can experience different delays on the two links and packets of a single call can use one link in one direction and the other link in the other direction.

Hope to help

Giuseppe