Citizenship application and HMRC tax underpaid letter

[t0mmy]

I am due to apply for british citizenship in a few months time. Currently on ILR.
I have recently received a letter from HMRC that I have underpaid tax by a certain amount. I am not sure how this has happened as I don't do contracting..am a full time permamnent employee of a large organisation and so my tax is deducted from my salary automatically. I have never had issues with tax.
The letter states that the amount will be deducted from april 2014 onwards by including in my tax code.
I realize that there is a requirement for tax reference code in the citizenship application to check whether the applicant has underpaid tax.
My question is do I wait for HMRC to deduct the tax by themselves(so I would have underpaid tax at time of my application) or pay now before I submit my application. It is possible that my employer hasn't paid their part of the tax however the amount is not that much and I don't want to drag my employer into this or prolong this issue till my application.