"Clean up" can refer to cleaning a mess such as putting toys away, wiping a messy table area, etc.
"Clean" (without up) us usually used in the USA when we talk about cleaning up something with soap or cleaning solution and water
"clear up" could include acne on your face (fewer visible pimples), solve or clear up a misunderstanding, mucky water may be starting to clear up (be more see through), etc.
"neaten" I have never heard or seen this word used before (I live in the USA). However, I would assume if I heard it that the person was talking about making something look neater. This could include a messy room, a messy paper (by erasing and writing more clearly), ect.
"put in order" could mean to put things back where they belong, put them in better places so they are easier to find, put them in a specific order such as alphabetical or chronological, etc.
The following are a few other similar words:
Organize
Tidy up
Put away
Again, my edit was only to fix my own typos.