First, make your classes to load the shader files. There should be methods to start/stop the shader, to wash (cleanup) the shader and to grab the shaders' program ID.
In your MainLoop (gameloop) After starting the shader for an object, type this in:
GL20.glUniformXf(GL20.glGetUniformLocation(shader.getProgID(), variablename), a);
Where variablename is the ...
There's nothing special you need to do for this - shaders work just fine with glBegin/glEnd code.
You create and bind shaders in the normal way, set uniforms in the normal way. You still need to pay attention to the parts of the OpenGL pipeline that shaders replace, but that's the case no matter how you do your vertex submission.
For reading your vertex data ...
What you ask is can be achieved by various ways i think
You can select your character's cheeks and mark them as another material in blender3d(3ds etc.).
Then only thing you need to do is use the same texture material with a red color tint.
You can paint your character's cheeks with a white vertex color in blender3d(3ds ...