Am planning to apply for Permanent resident under Canadian experience class, at the same time my company is planning to initiate my LMO process now, is there any conflict between these processes please let us know.
No conflict, go right ahead.
LMOs are issued by HRSDC in Canada. Your application for PR-CEC will go to CIC in Buffalo, separate agencies. You should get a response on your LMO before your PR file is even created by CIC.
CIC relies on Letters of Employment to determine if you have the required work experience - if you submit alternative proof, they may call the employer to verify. If this happens and your employer will be upset, it is a risk you will have to accept. If your employer fired you, you would be able to remain in Canada for the duration of your work permit (your employer cannot take that away from you), although you would not be able to work without finding another employer and obtaining another LMO.