About question 1:
The deploy target is irrelevant. It is only relevant for "normal" Worklight applications that are managed by a Worklight Console (so you must specify on which server your Worklight Console runs). But the Application Center client is not managed by any Worklight Console. All what you do is to build the environment, create the IPA and upload it to the Application Center server. Therefore, please only use the "Build all environments" menu item and ignore anything with deploy target!
About question 2:
The Application Center mobile client for iOS should be in the iphone environment, not in the ipad environment. The code in the iphone environment folder should work for ipad as well but you cannot generate an ipad environment for the Application Center client, as well as you cannot delete the iphone environment and regenerated it via File > New > Environment, because when you do that, the libAppCenterInstallerLib.a gets deleted. You must take the project as it was in your original installation.
Please check IBMAppCenter/apps/AppCenter/iphone/native/appCenterLib. This should contain subdirectories (for Release, Debug ...) which contain libAppCenterInstallerLib.a. The error message that you see means that it cannot find this library; probably because you deleted the iphone environment or because you attempted to create an ipad environment.