To setup a standard invoice, not the advance payment invoice, move your mouse over the Create new invoice button and click on it. Do not select the previously mentioned Create advanced bill option because then you'll be creating an advance payment invoice.
The beginning of the standard invoice creation is the same to the creation of an advance payment invoice. Select a client (to whom the invoice is going to be sent), fill out order date, order type, invoice number (bill number) and everything else that's asked of you.
Where things get interesting is the bottom section of the create new standard invoice form. Here you get to add items to the invoice. Start typing item details in the Item details field, and you'll be given autocomplete suggestions from the list of items (that you previously filled out). By selecting items from the autocomplete suggestions remaining fields (rate, tax, etc.) will fill out automatically. You just need to type in the item specific stuff yourself, like quantity, discounts, etc. Pay special attention to the Add advanced payment option at the bottom of the image above. This is where you can add a previously created advance payment invoice that you created for this particular client. That last bit is important to know because you will not be able to add advance payment invoices made towards other people (makes sense). If there aren't any advance payments created for the selected client, the list of advance payments is going to be empty and you won't be able to add any. Advance payments have to be created (and presumably sent) before the standard invoices are created. Which also makes sense.