It is still possible to check in using an e-ticket. Just go to the check-in counter, present the card you booked the etix on and say you want to check in. If the flight is overbooked they will ask you if you would like to Volounteer for Denied Boarding (VDB). This is recorded in your PNR as 'VDB' and you get called up at the gate if the situation gets critical.
Another way is to check in at the machine, then go to the gate early and offer yourself as VDB. The gate agents tell you if they are looking for people a that point.
Etix are not a problem for gate agents, although it involves some extra typing work to arrange for the audit coupons.
Regards Oliver