What exactly are you trying to alter in your audio ?
You can only Automate any controls that are available. So if you're using Sample Player to play your file about all you can automate is volume plus the controls of any FX you have in Effects Chain. If you're using AudioFileProcessor there are a few more options. But basically if you can't see a knob or button that controls what you want to change then you can't automate it.
Have a look at https://lmms.io/documentation/Automation_Editor and see if that helps.
Steve