Just need to know how i can start this

[BMR777]

1: Would i create a new table with the user ID and/or username, plus how much of each gem they have, or would i be able to add new fields to the "users" section already in place?

I would suggest making a new database table that records how many emeralds and pearls the user has along with how many clicks are required to get another emerald or pearl. Then in levelup.php you would have to run a check as the clicks are counted to see if the user has enough clicks to get an emerald or pearl. Then you would on your custom page whenever the user redeems one of these items, you would decrease their emerald / pearl count in the table.

2: Which files would i need to edit to make this happen?

Your custom file would need to be edited, along with levelup.php. You'll also probably want to make a new database table for this. :)

Hope it helps,
Brandon