Can I Use Auxiliary Optics to Improve the Emitted Beam
If you wish to produce a collimated beam, put a point near the center of curvature of the LED 'dome' at the nominal focal point of the lens. With visible LEDs, judge the results by eye. If you're working with IR, you can get feedback on the focusing process by monitoring signal level at the detector.....just work at optimizing it. I've listed a couple of other IR optimizing methods in the Beam Optimization Section below.
Regarding lens quality: don't be too concerned for a system of this type. Inexpensive molded plastic lenses work fairly well provided that you don't try to go lower than f2 or so.