@rahulbharate
Agree with @Hex on this is a personal choice, depending on how much confidence you have if you do it on your own.
In my case, my company HR helped to submit the employer nomination and I submitted my visa application myself, although we usually go through MA. It is to save some $$$ on MA's service cost for me. Our company used to pay everything of the visa cost. Now the MA cost goes to employee... With or without paying MA service, most info/doc for the application are still the same... To me, the guides on immi website is not too difficult to follow. As long as being honest and providing reasonable material in the application, I personally feel immi is not hard...
Anyway, it all depend on whether you believe you can manage the application yourself or not...