1. Yes, it matters. Upgrade priority is by elite level, then fare class, then Reserve card, then time of request. If you split the PNR 8 days out, your request will be dated then, as opposed to getting a bit of a boost by having done it 60 days out. Granted this is the 4th level tiebreaker, so the effect is probably only a couple slots at most, but it could make the difference.
2. Ask the agent to "link" your PNRs after splitting them. This is really just a note that you are traveling together, but it's as much as you can do with split PNRs. An agent who sees the note should try to reroute you and your companion together in the event of IROPS, but there are no guarantees.
3. The seats will "hold" but they will not be able to change to other EC or preferred seats, or to reselect them if there is an equipment swap and they are automatically reseated in standard seats. Some agents will seat your companion next to you in EC or preferred seats, but recently this seems to be limited to a spouse, not just any companion.