If you are seeing this error (Error generating R.java from manifest) in your Titanium when you launch the Android Emulator, then the issue is related to your 'id' tag in your tiapp.xml file.
You can change this from your Titanium Developer. Choose the project, and click on 'Edit' tab on top. Then under the 'Application ID' change it to com.yourcomany.yourproject (replace your company with your company name and yourproject with your project name). Should not have any spaces or special characters.
Then save changes.
After that, under your application folder, under build folder under 'Android' folder delete all contents.
Now from your Titanium Developer, select 'Test & Package'. Select 'Android' and then click launch. the application should work now.