I don't know if I'm understanding your question, but I serve .htc files for websites using Kentico:
In order to get Kentico to server up .htc file, you have to allow Kentico to process .htc files.
If you want to upload it to Kentico, then change the site manager > settings > Files > upload extensions to allow .htc
If you want to deliver .htc then add .htc to the site manager > settings > URLs and SEO > Friendly URL extensions
See help about URLs and SEObtw if you don't want Kentico to serve .htc, then you can just put the file in the root of your kentico website and let IIS serve it up.
Cheers,
Lance