The natural way to express that would be:
熊本行き(の電車)は何番ホームですか?
Replace 何番ホーム with どこ like you originally had and you'd still probably be understood, though the former makes it clear that you're explicitly asking "which platform" (like your English example) rather than "where is the train".
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A few pointers to remember in the future:
- ~行き (read as "ゆき") is a suffix meaning "bound for". It's a very common phrase to use with trains, flights, etc.
- を is a direct object marker. When asking where X is, X is not a direct object, so ◯◯をどこですか is not grammatical. (It would be grammatical in something like, for example, この椅子をどこに置けばいいですか?"Where should I put this chair?")
- 熊本は電車~ can never mean "the train for Kumamoto", as は is a topic marking particle, and not something that can connect the words 熊本 and 電車 . If you said 熊本は電車のホームはどこですか? (fixing the ungrammatical を), it would still be a nonsensical sentence meaning something like "Speaking of Kumamoto, where is the train platform?"
Hope this helps a bit.