I'm a COS and I book an extra seat all the time. There's a long thread on this subject on the PMUA forum. To answer the raised questions, here's the skinny:
1. Both tickets should be on the same PNR. one is booked with your real name (e.g. Bit, Big) and the other with your surname and first name Extraseat (e.g. Bit, Extraseat).
2. You should only put your MP# on your first ticket. I don't know about on the new website, but on the PMUA website it would reject if you put the same FF# on both seats.
3. Your normal mileage should post on your first ticket, both RDM and PQM. You need to save your boarding passes and fax them with an explanation that you are requesting mileage credit for the extra seat. You'll get RDM but no elite bonii or PQM for the second ticket. It usually takes them about a week after you fax them to post the second ticket's RDM's.
4. In the old PMUA days, after they instituted UDU, both seats would go in for an upgrade on any domestic legs, and they'd both ride the priority of the higher status (1K), so I'd often get upgraded to two adjacent F seats on domestic legs. Now, under the new COdbaUA policy, both tickets ride the lower status passenger's status, where Extraseat is not even an MP member, so I never get UDU upgraded any more (nor has my Kettle-looking Extraseat companion ever been offered a TOD upgrade, either!)
In the old days, I used to buy a single seat and use my SWU's to upgrade my international flights. Once PMUA went to lie-flat seats that shrunk the available upgrade pool space, and the minimum "W" fare rule came to be, I re-assessed my strategy. Since I usually book my international trips well in advance, I find I'm far better off with two E+ seats together on an S or T fare basis than paying a W fare (which can be almost as expensive as two T fares). Yes, I never get to enjoy an upgrade to intl C (which IMHO has become a "meh" experience), but I enjoy far greater peace of mind not worrying about whether or not I'll win the upgrade lottery, which is becoming increasingly difficult to do.