For practices that bill insurance, you can specify which specific ICD-10 diagnostic codes apply to which specific reimbursable charges (for the HCFA) when adding the charge to the applicable encounter note. Depending on your configuration settings, you may need to click to "Manage diagnostic justification for charge", or you may see the Justifying Diagnoses already shown by default at the bottom of that Add Charge window:

Diagnoses shown in orange/gold are formally associated with the charge as diagnoses that justify that particular charge. By default, all of the diagnoses that are in the encounter note Assessment box will be selected. 

Single click on a orange/gold diagnosis to disassociate it, turning it grey. Single click on a grey code to associate it. 

You can also double click on a code to disassociate ALL the other diagnostic codes, leaving only that code associated/ selected.