I added tags to this post to increase visibility.
Hi ChemBio20 - we would actually recommend using MassHunter Quantitative Analysis for doing quantitative work. It's more directly suited to doing what you're looking to do.
In general - if you have response of an EIC signal in your blank runs - there are two approaches to handling it:
1.) You have real carry over caused by inadequate flushing of your chromatographic system. (needle wash, column rinsing, etc) might be needed.
2.) You can subtract the response of the blank runs from your samples (Quant does this, Qual does not).
Hope this helps.