Yes for the javascript files, just make sure you create a sub folder in the Custom directory named the same as your site's code name (best practice). Then you can use the built-in tools to place the javascript on your page. Add a javascript webpart on your template and add this in the Inline section:
<script src="/CMSPages/GetResource.ashx?scriptfile=/CMSScripts/Custom/<sitecodename>/Cycle2.js" type="text/javascript"></script>
For the stylesheets, you have more control of them by using the the UI Stylesheet application. By default IIS will load any .css file in the App_Themes directory. What I do is create the main site stylesheet and name it the same as the site code name (best practice) and assign it to the site. Then any other stylesheet will simply be added in the UI and named as you wish. Then you can use the HEAD HTML webpart and add a new stylesheet in the order you need them by using this syntax:
<link href="/CMSPages/GetResource.ashx?stylesheetname=YourStyleSheetCodeName" type="text/css" rel="stylesheet"/>
Using the GetResource.ashx will allow your end file to be minimized as well, which is another bonus.