Click on the items that pop up to add them to your inventory (on the left). Once they are in your inventory, you can use them! Press 1 to use your Swords (Costs no mana) Press 2 to use your Potions (Costs 10 mana) Press 3 to use your Thunder Spells (Costs 10 mana) Press 4 to use your Fire Spells (Costs 12 mana) Should the Boss Charge reach 100, it will either deal massive damage to you or he will heal himself (But not past 10000). By the way, there might be a few bugs (like the items appearing for a milisecond and then disappearing) but there isn't much I can do about that. This is moreso a fault of Scratch itself rather than the coding. Sorry!
Swords deal a little damage, but spawn frequently and cost no mana. Potions heal yourself, but you cannot heal yourself past 1000 and they require 10 mana. Thunder Spells deal a lot of damage, but they require 10 mana. Fire Spells deal the most damage, but they don't pop up often and require 12 mana.