You can customize the directory when you are creating the portal, for example, we have an installation that is from a corporate level to franchise owners. Each owner has there own number. As we add portals we just tell dnn to create them in the portals/(InsertFranchiseNumberHere) instead of portals/[PORTALID]
Just one warning about this otherwise sensible and logical step - Module developers are occasionally unaware of this feature or simply ignore it. I have always used friendly names for the site folders yet have had modules that fail to function because they only recognise the numerical ID when accessing the portal folder. This is usually made obvious in the error message or sometimes the module goes ahead and creates and uses it's own copy of the numbered portal folder.
I'm currently waiting for 2 commercial module developers to fix this in products I have purchased. Although now, because I'm starting from scratch for the n'th time, I'm probably going to revert to the default DNN ID numbers in order to spare me any more unknown future dramas with this.
And while I'm providing warnings - Do not rename modules to your own standards of communication. Again, some developers haven't taken this feature into account. Some modules won't upgrade properly and won't uninstall either. Just ends up in a mess and there's no way to predict it until it happens.
I'm sharing this here, because I'd have a couple of week's spare time on my hands without these un-necessary problems.
As for the main quesotin in this thread - definitely work towards multi-portal instances. You have to raise your level of care and accuracy in everything you do, but overall the work should be far less... should be.
Rob