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No, don't add anything for free. I haven't run an alchemist so am not 100% on how it works, though. You will define batches from your available formulas. Those will use your daily allotment of reagents. You'll click the + icon next to each batch to create it as part of your daily preparations—that will add it to your alchemical equipment under infused items created by you.
I don't know if those automatically go away after a night's rest (it doesn't look like it when I try and test it), so if you change up your daily batch setup you may need to delete some infused items and refresh the batch the next day. Hopefully someone from Lone Wolf or who plays an alchemist can give you better details.
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