It sounds like you have a good approach planned.
If you are going to go with the premium account for now, you can also note specific cards that are in a given deck. I like to keep track of what cards are in each deck, as it helps figure out where specific cards are and where I still need to upgrade cards to foil.
The ability to easily add cards to specific sets with the + and - buttons is wonderful. Just make sure that you set your default values properly before you do. You'll probably want to set NM as the default condition and specify that your cards are in English.
For proxies, I would suggest marking them as textless cards. There is no legitimate reason to use that property any longer, so it makes it very clear that something unusual is going on, and you'll also have an easy way to filter your collection as well. You can just filter your inventory for textless cards and see them all really easily. If you want to get a rough idea of your collection value you can filter your inventory to not show textless cards, and then select 'View' -> 'Total Set Value' to get the value. Just note that Deckbox values aren't great. But, as you said, you'll have your inventory available as a CSV, so you can get a more accurate estimate of card value elsewhere.
Okay. As soon as I entered one card, I think I see a problem with my plan heh
I picked up a deck. Sorted it. Went to input it. But it looks like there isn't any way to enter the deck, and in doing so add it to my inventory. If I just put in the deck, it just warns me I don't have the cards to make the deck. I can tell it that the cards have to be in my inventory, but that's kind of the opposite of what I want.
Am I missing some way to simultaneously add a deck and add the cards in it to my inventory? It'll be a drag if I basically have to enter all my decks twice.
EDIT: I think I found it. There were multiple interfaces to add cards to a deck, and I think I just found one that will let me add to the deck and my inventory. It is a premium feature, but I think I was going to end up needing a premium membership anyway.