There are no problems store all your css and JS files in your solution. (it could a problem NOT to have css... ;-) ) Just create folders for your content, put your files in there and reference them from your code. All references are standard .Net with / beeing your site root...  You can also use ResolveUrl method in System.Web.UI.Control to get your file paths. Eg. <script type="text/javascript" src="<%=ResolveUrl("~/Scripts/js/jquery-1.3.2.min.js")%>"></script>

If your question is if it is possible to place your css and js files in the %programfiles%\EPiServer\CMS\X.X.X.X\application folders, the answer is yes, but I'm guesssing it is not a recommended solution. You can create virtual paths for a folder and share that folder between several solutions. (if you have more than one solution using the same js or css files....)