The Travelocity fares that we received as part of the package were eligible for upgrades. And yes, they did earn miles, elite bonuses, 500 milers, etc.

There are other threads on this "phenomenon" of packages being less than flights alone. I myself have only bought from Travelocity, but others have reported success with United Vacations. From these providers, when buying DOMESTIC (including Hawaii) packages, I have never heard of anyone being refused miles or the chance to upgrade. If you are booking an international package, then that's a different story, because the upgradable booking classes are much more restrictive. But even then, I have never heard of someone notgetting the miles. UA is very good about mileage accrual on their metal (except for Priceline and Hotwire tickets, of course.)

If you're afraid of not getting the miles or the upgrade, perhaps try calling the package provider, ask them what the fare basis of the tickets is, then call United and ask them if you can earn miles/upgrade. But honestly, for domestic travel, this is really not much of a risk.

One other point: if you buy your tickets (flight only, not a package) from UA, you can refare your ticket and receive refund vouchers if the price drops. Once you buy the package, you've locked in a price and can't refare if the price drops. Just FYI.