There is nothing wrong with BYOD in general. In fact, if your ATA/analog phone combo suffers from echo or other problems, BYOD is better, assuming it is an IP-only device.

If your iPhone is 3GS or newer try Bria. Sound quality is great. If X-Lite on your PC sounds bad look at your headset/microphone.

I use all the above and have great results. Something is wrong with your setup.