If you install a skin, it will use a new set of templates and hence anything you've added to the hacks via the templates will not show on the new one. The ACP tells you what template files you've edited, so its your job to go through and add the code to the new templates.
If the skin you're installing is just a colour change and nothing changed to the templates, it can be a child style to the current set of templates you're using.
This is also a support thread, so moving to General Mod Questions.
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