We live in KS and our Nebraska income and estimates we paid are showing up in Ks and not being applied to NE?

If you have Nebraska income in 2017, but maintain your home in Kansas, then you will need to file a Non-resident return for Nebraska and a Resident return for Kansas.

Once you've determined that you need to file a nonresident state return, the first thing you want to do is make sure you've filled out the Personal Info section correctly:

• In your open Federal return, choose My Info in the left bar
• Continue to the Your Personal Info Summary screen.
• Scroll down to the last section, Other State Income, and Edit.
• At the first screen Did you make money in any other states? answer Yes and make sure your nonresident state(s) are selected from the drop-down menu and Continue

Then, 

• In your Federal return, under Deductions & Credits, 
• Scroll down to Estimates and Other Taxes Paid and Show more
• Start/Revisit Estimated Tax Payments, then choose State Estimated Payments
• On the page How much did you pay in state estimated taxes? you will be able to choose Nebraska from the dropdown menu and add the date and amount paid.

Be certain to complete your Non-Resident Nebraska return before your Kansas return, to make the allocation (division) of income and credits easier to navigate.