If they are two different installations of DNN then it's trivial - so let's assume it's not that.

Best practice is NOT to change the original files.  If you do that then every upgrade will overwrite your files and you will have to reapply your changes.

Here is what I would do - it's easiest.

Find the folder - Portals\_default\Containers\DarkKnight.

Copy the container Aside.ascx TWICE to make AsideCustom1.ascx and AsideCustom2.ascx.  Make your customisations in those files.  In portal one set the default containter to AsideCustom1, in portal two set it to AsideCustom2.

If you need css overrides that are specific to the customisation then create a (say) AsideCustom1.css and add them in there.  They override what's in container.css.

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Best wishes,
- Richard
Agile Development Consultant, Practitioner, and Trainer
www.dynamisys.co.uk

Thank you both! Sounds I'll give both these a try.