I consider these very nice speakers for the $150 or less you should have paid.
With 3.5" woofers, the bass is missing, but the mids and highs are quite nice!
I have used them with a sub to fill an office with good sound without any issues.
The sub I used was a Velodyne VMS-8, but I am surprised that any sub wouldn't reach a level that balances with the speakers.
What are the source(s) you have hooked to the Ceres 3.5's and how are they connected.
Where is your iPhone volume set, where is the Ceres volume set, and where is the sub volume set when the sub sounds good?
The "Low Pass" knob on your sub should be at around 2 o'clock to crossover well with the Ceres 3.5. See if that changes the way things work in any significant way (though I wouldn't expect it to unless Don G.'s theory is right and you currently have it set to 180 - as high as possible).
BTW, there is no manual for this product. It only comes with a "Quick Start Guide" which can be viewed here:
http://static.bhphotovideo.com/lit_files/105077.pdf
However, it offers no information that is useful for evaluating the gain structure.