How can i create a manage and unmanaged package from force.com IDE (from Eclipse) by default when i deploy from one org to another org (via IDE - Deploy server menu), its unmanaged package able to read all the apex class from the destination org
You can't create a managed package in a new org via the Force.com IDE, as that has to be done in the UI. However, until we have DX, you won't be able to share the namespace for your package in multiple developer orgs, so all development orgs except for your packaging org would have to be unmanaged. You can deploy unmanaged packages from the Force.com IDE.
How can i pull (in IDE) all the apex class from managed package org (assume that org was managed package)
When creating a new Force.com Project, select the "package" option and choose your managed package. It will automatically select all items in your package, and place them in your project.