Actually there is no standard procedure for ordering checks because the church knows what checks you've been issued and what checks you've written and automatically sends new checks when you get low.
However, that should have already happened long before you're down to 2 checks (we received new checks a few months ago and we still had about 100 checks left). So first check with your bishop to make sure he doesn't have the checks around somewhere that you don't know about.
If you can't find them then you need to call the
Global Service center and ask them about the issue. They should be able to say whether you've already been sent checks and when they were shipped. If for some reason they haven't been shipped they can initiate a shipment (but it will probably take a couple weeks for the printing and shipping but maybe they can put a rush on it). If the checks were sent and lost then they'll have to both initiate another shipment and put a stop on all those checks that were lost.