W2

To answer this question, I'm assuming that you are a resident of Kansas (KS).  As a Kansas resident, all of your income is taxable by Kansas regardless of where it was earned.  If you work in Missouri (MO) as a non-resident, the income you earn in MO is taxable by them.  Since all of your income is taxable by Kansas, you will report 100% of it as taxable income on your Kansas resident tax return - $47,000.  On your MO non-resident return, you will report $31,899 as income taxable by MO.  To prevent you from being double taxed, KS will give you a credit for tax paid to MO.  The credit will be the amount of KS tax on that amount, so it may be less than the amount you pay to MO, but it will not be more.  So, the way your employer allocated your earnings is probably the best way to do it, assuming your KS tax on the income earned is MO is approximately the same or more than the actual MO tax you have to pay.

When completing your state tax returns, you should complete your non-resident MO return first and then your KS return.  This will result in the KS credit for tax paid to other states being properly calculated.    

I am having to pay in KS tax about $400  even with credit from MO.. My employer only taxed what I earned in KS  on the $15,612 

I recommend  you monitor your tax withholding periodically throughout the year (at least quarterly) to make sure that your tax withholding is being done correctly.