You create your own MDX (that's the other acronym that is used a lot) account and then you can link everything to it.
When you purchase via a third party reseller, you can save a lot of money, but there are some differences. It is a Disney reservation but you didn't buy from Disney's inventory. You bought from inventory that was sold to another company by Disney, so they could resell it.
You can't purchase a package reservation via a third party reseller. So you have to get your tickets some other way. You can buy them via Disney or you can go to an authorized ticket reseller which might offer you a bit of a discount. Either way the tickets you buy can also be linked to your MDX account. Even if your resort reseller offers Disney tickets and you buy them that way, it's not a package reservation, it's a separate purchase.
And because you can't purchase a package reservation, you can't get a dining plan, if that is something that you are interested in.
Some of the differences are:
With a reseller, you must generally pay in full when you reserve.
If you want to apply a different discount or change your resort or dates, you must cancel the previous reservation and book a new one. Make sure you check to see if the reseller will charge you a fee for cancelling.
You must link your reservation to your own MDX account. The reseller may not outright give you the proper confirmation number needed to do this. Although there are a lot of things WDW won't do with a third party reseller reservation, they have been helpful to me when I have had to ask for the Disney confirmation number on my reservation for purposes of linking it to MDX.
If you are booking with children, check and make sure that they don't charge fees above 2 people in the room for children. IF your reseller does this, you can fix this by just booking for the adults, and call the reseller later. They would need to call Disney to add the children without there being an extra fee for them (which Disney doesn't charge when you book through them). 18 and older count as adults on a Disney room reservation and if there are more than 2 persons aged 18 or older on the reservation, the extra fee would be paid on the additional adults anyway. So if you need to do this, it pertains only to minors under age 18.
If you are in need of Magical Express airport transportation you will need to add that manually by calling Magical Express or using the online form.
When you are customizing your Magic Bands, make sure you check the shipping address. On reseller reservations, this usually defaults to the corporate address of the reseller; make sure you change it to your own address.