I have a groove in both side panels so that my 8mm back slots into this. So the groove is from top to bottom and 8mm wide, 5mm deep. The thing is I dont have an 8mm wide tool set in my router so I'm not sure of how the machine will cut this, has anybody had any simular thing happen?
Will it use my 6mm tool and create a double pass to create the 8mm groove, or will it just throw an error?
If your tools are set up correctly, the machine will select the next smallest tool and make two passes. Remember, always check your sheet thickness before sending the job to the machine. 8mm stock may not always be 8mm. When you select CNC in eCabinets, you can change material thicknes to the actual thickness, like 7.54mm.
Adding one more thing to Davids comment. I would go ahead and set your material up in ecab with the correct thickness and then build your cabinets. Sometimes changing the material thickness when writing the code can cause problems at the machine. Also your face frames will fit more accurately if they are referenced to the correct size material. I like to flush out my partitions with my face frames so that drawer slide installation goes easier.