1. Most likely you would want to check this box. If you do not, the taxable and subject to amounts are recalculated and added to the numbers already present for the employee(s). Checking it tells the system to clear the totals and recalculate from zero. The only situation where you leave the box unchecked is if you are using named transaction files, which is not very common. If all the checks for the employee(s) are stored in a single transaction file (IE the Current.prt file), check the box before clicking start.

2. It is important to restore your tax file to the file used for 2015. If you do not, then the subject to amounts will recalculate to the 2016 values. This means if any taxes had limit increases between 2015 and 2016, your subject to wages would recalculate to the limits for the new year, not the prior. You should only check this box if the 2015 tax file is in place before you recalculate the taxable and subject to amounts for the 2015 tax year.

There is a lot of good information available about this procedure in article 20556 in the Technical support knowledgebase, but I would recommend contacting customer support for assistance if you haven't done this before.