To view the commuting data for your region, go to Explore > Social Accounts > IxC Social Accounting Matrix. If the Employee Compensation column makes a payment to the Domestic Trade row, then there is net in-commuting into the region (more income earned by workers who work in the area and live outside the area than vice-versa). The ratio of this value divided by the Employee Compensation column total gives you an estimate of the net in-commuting rate. If the cell is empty, then the region has net out-commuting, which will show up as a payment from the Domestic Trade column to the household rows. To get a net out-commuting rate, divide the sum of these payments (across the 9 HH types) by the sum of the household column totals.
The equation below allows you to adjust IMPLAN's estimated regional commuting rate to your known regional commuting rate.
newEC = EC*[(1-userCR)/(1-samCR)]
EC = original, unmodified employee compensation
userCR = your known commuting rate
samCR = commuting rate reported in the SAM
newEC = the EC value you want to use when running the analysis
For example, if the SAM shows that the average commuting rate in your region is 10% but you know that for your industry it is 20%, then: new EC = $1,000,000*(0.8/0.9) = $1,000,000*(0.88888) = $888,888.
After the scenario has been run, add the difference (EC - newEC) back to your direct EC effect since by definition EC occurs at the site of employment. Since EC is a component of Value Added, you should update the calculation of Value Added to include the difference. This way you correctly account for the in-commuters' direct effect, but you have also made sure that they did not generate any further local impact.