So it sounds as if you're using ASPX development mode, any particular reason why? I'd suggest using the Portal development mode. It allows you all the same flexibility with less code to write and maintain and take advantage of quite a few more out of the box features. You might also look into using v8.2 vs. v7 as v7 is over 3 years old now and v9 will be coming out in a month or two so save yourself the headache of upgrading later when you can do it now pretty painlessly.
If using Portal mode you can simply place a webpart on a page template and add stylesheets and js file references from within there. Check out this reference on how to setup your folder structure within the physical file system (the majority of this is automatically setup if you use the correct naming conventions within the UI).
If you want to take advantage of the minimization and caching you can use the following lines of code:
Stylesheet in file system:
<link href="/CMSPages/GetResource.ashx?stylesheetfile=~/App_Themes/MySiteCodeName/foundation.css" type="text/css" rel="stylesheet"/>
Stylesheet within the UI:
<link href="/CMSPages/GetResource.ashx?stylesheetname=StylesheetCodeName" type="text/css" rel="stylesheet"/>
JS File in the file system (can also be seen in the UI)
Keep in mind if your site code name is "MySite" and you have physical files within the /App_Themes/MySite directory, by default ASP.NET and IIS will automatically add them to your page, this is standard functionality of an ASP.NET website. If you want more control over them I suggest using the Kentico UI.