Of course you would have to rename the folders accordingly if you set the software to use custom names.
What Zachery means is more general: It does not make a lot of sense to use that option at all. There is not much security through obscurity, especially if you just replace i by 1 and o by 0, which has to be the oldest "encryption" trick there is.
You're much better off doing what he proposed: Create a .htaccess-file and protect your admincp folder with an additional password, and if you have a static IP, you can set it up so you don't even have to enter that password if you're working from your own computer. Protecting modcp in this way is not that important - there's not much harm that can be done from there.
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