You need to provide more specific information about your question. What is the purpose of the withheld tax? Is it tax on income a customer is required to withhold and pay to the tax authority on your behalf? Is it VAT you are being charged on a purchase? Is it VAT on an import that was not paid to a supplier? All have different implications. Provide an explicit example.
As for how you enter amounts, if you are using the correct transaction form, virtually all entries to Manager will be positive. Manager figures out whether to add or subtract them to posted accounts based on context.