Engraving machine drivers have a concept of Roughing tools and Finishing tools.
When cutting out a piece of material with an engraving machine the majority of the work can be done with a Roughing tool, leaving a small amount of material at the sides and the bottom to be finished off with a more accurate Finishing tool. You can specify the amount of material to be left for the finishing tools on the Engraving Machine Settings page. A different value can be specified for each of Crease Channels, Area Clearance and Location Holes. Also, a different value can be specified for Sides and Bottom.
When configuring a tool in the Tool Settings you can specify how it is to be used from the Tool type list.
When configuring the Sequence Attributes you should choose a Roughing tool for Tool 1 and a Finishing tool (or <None>) for Tool 2.