Can I apply for AEO immigration after I submit my application for skilled migration?

Yes, AEO is not an individual application. It is your local employer who is willing to hire you to apply for a job arrangement with the Canadian Human Resources Department, so all the expenses should be borne by the employer. If you just want to work with a local employer, you should discuss his expenses with your employer. Generally, the current market is around 6000- 10000 Canadian dollars.