Hi Vikash,
Please find my comments below
1. Will it effect existing user in EEM having same userid as in AD.
MK: When you talk about existing User, are they part of EEM local store? If you are configuring to AD for the first time then it will move the EEM connectivity from Local store to SD store (reference to AD). So you will no more be able to connect using the local store users if pointed to AD
2. How can I assign default Application group(PAMUser) to all the imported AD users.
MK: If you have added the default application group (PAMUser) to the AD users then you can automatically import all the users with the same settings.
Let me know if this helps?