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 and/or Foreign Trade row, then there is in-commuting into the region (income earned by workers who work in the area and live outside the area). The ratio of Domestic plus Foreign trade value divided by the Employee Compensation column total gives you an estimate of the in-commuting rate. This rate is referred to as the "samCR" below. If the cell is empty, then there is no in-commuting into the region.
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 in-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 analysis 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.