First, be aware that UA vacations is simply a travel agency that basically buys access to the United name, and does the package deals. Really, it's not different than booking a vacation through, say, Orbitz. Except that I believe they'll only sell UA (and perhaps, partner) flights and have access to whatever inventory they do.

There is a place when your doing the search where the published fare (or bulk fare) gets linked, and if you click on it, it gives you the detail of what it is - so most of what you need to know is there. Anything noted as a published fare will earn PQM, PQS, RDM and PQD as normal based on the flight prices. Like any travel agency, however, any changes need to go through them, especially as these are packages, but using your MP number, the flights should appear on your profile on the UA site, and you should be able to select seats, etc. as normal. And yes, tickets should be on 016 stock.

Bulk fares are different, and would earn miles based on the bulk fare chart, and also wouldn't get PQD. If it's listed as published though, you'll get the same treatment, essentially, as if you've booked directly through UA.