VIP upgrades work on up to 3 segments as long as they are transits. In your case the first VIP upgrade is good for SFO-ORD-MAN and 2nd one for the return. You could have had a routing like SFO-DFW-ORD-MAN and it would have upgraded all 3 segments with one VIP. So you didn't waste any VIPs and the domestic upgrades are free for EXPs so you didn't waste that either. An advantage with the VIP is it is likely to be confirmed before the 100 hour mark.