This is up to you.
What detector are you using?
UV variable wavelength
Could you tell us which version of Chemstation you are using and maybe share a picture of the chromatogram that is causing you a problem. It would also be great to see the integration settings that are used to measure your peaks.
It sounds to me that you are using classical baseline correction with too narrow a peak width in the integration parameters. Only a guess without seeing what you are actually doing.
I wouldn't apply manual integration, but change the integration parameters so that all peaks are integrated automatically.