You setup your armor on the armor page. Using the buttons underneath each armor piece set the armor to the same level that you have in game. If you haven't upgraded a piece of armor at all yet the correct level is "Base".
If there are any pieces of armor that you don't have yet and wish to exclude from the results you can simply mark them as "Ignored".
You setup your inventory on the inventory page. Using the input underneath each item you can set how many of each item you have. For small tweaks you can also use the increment and decrement buttons at the end. Progress is measured against the goal of getting all upgradable armor to level 4.
If you've visited a great fairy to upgrade your armor you can quickly update everything using the upgrade button on the armor page. This will automatically consume the required materials and increase the level of the armor. If for some reason your tracked inventory is short on materials (for example if you forgot to add some recently farmed items) it will consume as much as it can setting the amount to 0.