We normally add the taxes that are collected by companies which means:Value Added Tax, Import and Export taxes (you should create a tax rule for them) and so one.
Does company have the possibility to substract this taxes from the tax they collected? You should add them if the answer is yes.
As far as this is included on the invoice (this is the case in Spain) you should add them and ad a tax rule to be set on the self employed parties. If you want an example this is called Retencion taxes in Spanish Chart of Account.
I think you should use taxes and account as defined by tax authority always using the full name. This is the way that most accountants will find them.
P.S: If there is a code defined you should also set them on templates as most accountants will refer to accounts by it’s code.