Thank you for taking the time to evaluate HelpStudio.
1. Yes, you can. The link format will depend on how you are intending to deploy your help - if it's in plain html web help format, then the links will just be a relative url pointing to the topic in the other project. If you are deploying as compiled .CHM files then use the specific page in the link designer to create the link. Let me know if you get stuck.
2. You can create a project template from the currently open project using the "Save as Project Type" from the application menu (the menu that is shown when you click the top left button on the ribbon).
3. You can use the Content Snippets window for this exact purpose - create your Content Snippet using the "New Content Snippet" toolbar button and you can then include it in any topic from the Context Menu in the topic editor.
Let me know if you need any further information at all.