IANAL but my understanding is:
If you incorporate GPL licensed things into your software, those pieces must stay licensed under the GPL. The means: you must provide copies of those "modules" to anyone who asks for them. If you modified them, you must provide the modified copies. Finally, you have to include a copy of the GPL for those parts of your application when distributing your application. There is a minor misunderstanding among some people I've talked to that if you use GPL licensed software, your entire application defaults to a GPL license. This is not true.
In your case you have an aggregate work. Aggregate works are covered in section 5 of the GPL-v3:
A compilation of a covered work with other separate and independent
works, which are not by their nature extensions of the covered work,
and which are not combined with it such as to form a larger program,
in or on a volume of a storage or distribution medium, is called an
“aggregate” if the compilation and its resulting copyright are not
used to limit the access or legal rights of the compilation's users
beyond what the individual works permit. Inclusion of a covered work
in an aggregate does not cause this License to apply to the other
parts of the aggregate.
As you can see, the solution to using GPL material in your application is to modularize your application. There are the parts you wrote which you are selling, and they simply rely on other GPL parts -- which you are merely distributing, modified or not. You're not charging for jQuery, you're charging for a CMS that incorporates jQuery.
The other route is a SAAS model. Don't even sell the software but sell the services it provides (and related support for those services). This is, in my opinion, the most popular model currently. In this model, your intelectual property (well business model) is not the software (IP is irrelevant). You write the software, and then you become the best provider of its services to your customers. This is how Github, Bitbucket, etc. work.