On the Settings Tab of the Inventory Count Template you can either set this template to use the Location Inventory Count Settings, or you can use the override functionality.
Click the Use Location Inventory Count Settings button to "inherit" variances.
OR
Click the Override Location Inventory Count Settings radio button to set different variances.
Make any changes to the Count Settings Fields.
Count Settings Fields
Maximum Iterations - The maximum number of times that the inventory count may need to be performed. For example, if this number is set to 3, and the first count fails the variance, then 2 more counts may be done, if necessary.
Max Variance % (Number of items) - The Max Variance % (Number of items) is the maximum number of items per SKU by which a count can be off.
Max Variance Amount ($) - The Maximum Variance Amount is the maximum dollar amount of the difference between the manual count and the system count for a specific item.
Recount Products Outside of Variance Only - Check this box to indicate if only those products that are out of the recount variance need to be counted again.
Count Discontinued Items - Check this box if items that are classified as discontinued needed to be included in an inventory count.