Creating folders in the Applications folder

Question

I like to keep things neat in my computer, so when I started to have too many apps, I decided to create subfolders within my /Applications folder and move tings around.

Sometimes, I got asked to enter my password.

Sometimes, softwares upgrades won't work. Or sometimes they create duplicates. Sometimes things seem to get messed up.

I guess my question is, is it considered good to create folders there? What's the best way to handle this?