I figured out how I can do what I'm looking for but can't actually post the answer for 8 hours so I'll answer it here.
I was able to add the .c files as "Linked Resources" to my project.
So in the end I had an include path to ~/myfiles and a linked resource ~/myfiles/customlib/myfile.c.
Linked Resources can be found under Project Properties -> Resource -> Linked Resources -> Linked Resources(tab)
Unfortunately, my environment, Code Composer Studio 6 on Ubuntu would not allow me to actually add a linked resource through the IDE.
As a workaround I added the linked resource directly to the .project file.
~/workspace/myproject/.project
Under the section labeled "natures" I added
<linkedResources>
<link>
<name>myfile.c</name>
<type>1</type>
<locationURI>$%7BPARENT-2-PROJECT_LOC%7D/myfiles/customlib/myfile.c</locationURI>
</link>
</linkedResources>
The "$%7BPARENT-2-PROJECT_LOC%7D" refers to ~/workspace/myproject/../../ (a.k.a. ~/). The 2 tells it how many ../'s
In case you don't get the locationURI right the first time you should be able to edit the file path from Project Properties -> Resource -> Linked Resources -> Linked Resources(tab)
You can use any defined build variables for the locationURI. Here is another way to write the location URI. PROJECT_LOC/../../myfiles/customlib/myfile.c
Since this is an eclipse project file it will be overwritten with whatever eclipse decides is the proper format for locationURI
You can place the linked resource into a folder in your project by modifying the tag. projectsubfolder/myfile.c. This will create a folder projectsubfolder under your project directory. ~/workspace/myproject/projectsubfolder
Unfortunately this isn't an optimal solution as I will need to add linkedresource entries for every source file I create in my custom lib. CCS fumbles the linked resources when doing a project copy/paste, requiring you to add the linked resources again to your copied project.
In the end it feels like a solution but it really doesn't have much benefit over symlinked files. The only one being that when I copy/paste a project I will know the project isn't using the correct files when it doesn't compile. (symlinking will make a working project with copies of the files instead of the originals)
I imagine I will need to learn about creating .lib files to make the inclusion a little more pain free.