Invoices can be confusing. You just want them to add up to the right amount, modify it to look a certain way or just get a total so you can accept payment. There are three major ways to adjust invoices once they have been created. Note: This article does not cover adding more items to the invoice.
RECALCULATE THE INVOICE: when an invoice looks like the math is wrong or you added items, deleted items, added discounts then deleted an item, etc. and you just don't think ASAP did the math correctly, use Recalculate Invoice. For more on this, read this article: Invoice Not Adding Correctly
MAKE ADJUSTMENT: when there is an invoice item and it is not the correct amount (maybe it should be higher or lower for some reason), you should use the Make Adjustment link at the bottom of the Invoice Detail page to reduce or increase that invoice item. Adjustments are done one invoice item at a time. For more on this, read this article: Editing an Invoice
APPLY DISCOUNT: when you just want to reduce the amount of the invoice and don't care which items are reduced (as in all of them, or lots of them and you just don't have the time to adjust each invoice item), then apply a discount. Be sure you have a coupon that is set for % or $ and has a good name for the invoice descriptoin. Then apply it. This will reduce the full amount of the invoice and is easy and simple. For more on this, read this article: Working with Discounts