You always do it half-baked.

You always do it not thoroughly.

Are they correct and carry about the same meaning?

Same meaning. However, 'you never do it thoroughly' is much more natural.
>You always do it half-baked.
If you're using this separately from any context, I'd say:
You always do things in a half-baked way/manner/fashion.
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Thank you so much, Philip.
Generally, "half-baked" is used to describe a person or idea (adjective)

"She came up with this half-baked idea for the party."

Not "how" something is done.(adverb)

However, I have seen, "He did the job half-a$$ed."
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 Marius Hancu's reply was promoted to an answer.
Thanks, Sujankay and Marius.

Got it!