If you would like to employ more third-country nationals than you are allowed to by the quota, you need to request the permission of the authorities by submitting a labor demand to the local Labor Office when you are submitting the work permit application for a given employee-to-be. Then, the officials will evaluate whether the position should be filled by a local or by the foreigner in question. If the labor demand is approved, you can hire your candidate and they will not count against the quota.
A labor demand is not an obligatory part of a work permit application, but it is useful to submit both if you expect the number of your foreign employees to exceed the default limit. Please note that an approved labor demand only allows you to hire the third-country national for whom the labor demand was filed and no one else. If later on you decide to hire another third-country national for the same position, the labor demand must be submitted again.
Submitting labor demands is a common practice for companies hiring non-EU workers, which explains why some foreign business owners could have been surprised to hear that the number of third-country nationals they can employ is limited by default.