You can get a plane from Bangkok to samui and there are quite a few a day with bangkok airways the other carrier is Thai. The flight only averages an hour.
You would have plenty of time as the last plane is not until around 8 or 9 at night.
Certain carriers let you book your luggage through from your start destination right through to Samui.
The flight is not cheap though apart from usually the last one of the day. Check out the web site for bangkok airways and Thai domestic.
If you decide on the train I would recommend a taxi steer clear of the ones as you just arrive as they will offer more expensive ones you need to go downstairs and out.
I personally would fly but this will depend on your budget. Bear in mind to add your taxi fare to your train ticket fare to make a proper decision.
I don't know where you are flying from John but it is usually a pretty long flight to Bangkok and to add another overnight on that could be gruelling but hey if you can sleep anywhere and you are young enough you will be fine.
Enjoy

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Kiss
God laughs at people who make plans.