We do not have recommendations regarding debug IDE over USB. Usually JTAG (Lauterbach, ARM DS-5 DSTREAM) is applied. Customer can try using relatively simple command line application, such as sdphost. The sdphost tool provides a command line interface for sending Serial Download Protocol (SDP) commands from the PC host to NXP i.MX devicesin the serial download mode.
You may look at section 4.2.1 (SDPHost downloads Flashloader image) of the following app note reagrding example how to use it.