The Clear Area value is used primarily when calculating your crate dimensions By CONTENT DIMENSIONS. The value entered in the Clear Area field in Preferences > Settings > Clear Area is added to the Content Dimensions when designing a crate. This extra space ensures that the crate is not too small for the content item. 

 When creating a new design, in the New design window, you're able to see your default Clear Area values in the More Dimensions tab.  You are not able to reduce or increase these values here, you can do so after creating the design.  

When adding a Floater Deck you may need more clearance on one side versus the other. Example: you have a content item that will sit on a floater deck that has a protrusion on one side. So instead of centering the floater deck on the base, you need it moved closer to one panel to allow for the protrusion. In the image below my Clear Area setting is 5". Crate Pro adds 5" to each side of the content (excluding the base). My content has a protrusion on the right side so I adjust the Right side value to 9" which makes the Left side value 1". These values can be changed once the design is created. 

When Content Dimensions are used as your Dim Basis (See Preferences > Settings > Dim Basis), when any padding, wrapping, floater deck or other automatically calculated Packing material is added, users will need to LOCK the design to allow Crate Pro to re-calculate the updated dimensions of the design. The Clear Area value will be added to the Content Dimension + the thickness of the Packing Material.

When the design has been created  you're able to see the calculated Inside Dimensions from the Wts & DIms tab.  Content Dimensions + Clear Area value

To change the pre-set Clear Area - after creating the design, go to Packing > Floater Deck Position and adjust the fields as desired. Note that the Container tab light has been activated.  The inside dimensions will not automatically recalculate, click on the yellow light which takes you to the Container > Rules tab and RUN ALL RULES. This will recalculate the lumber and plywood rules. If any panel is lumber sheathed with lumber battens, you will click on that panel tab to run the rules on that tab. This give you the opportunity to decide if you want to adjust the CLEAN FIT, GAP or RIP values based on the dimension changes.

In Preferences > Settings you can set your default Clear Area values. By selecting the Checkbox next to Dim Basis - users will have the option to change the default dimension basis setting when creating a new design.