The auto-tuner in your radio might be useful for tuning the -input- to the amplifier, sometimes the amplifier's input could use a bit of tuning. But if your amplifier needs a tuner to match the antenna, I'm afraid you will need to find another tuner. Naturally, that tuner between amplifier and antenna should be capable of handling whatever the output power of your amplifier happens to be. It's always nice to have more power handling ability than is required, so a 'larger' than required tuner would certainly be nice.
I have a feeling that you may be 'across the pond' from me. If so, then I'm not sure how things are done where you are. Here, tuners are usually rated in power handling ability in Pep watts, not avg/RMS watts. That means that an advertised rating of 1000 watts really means 1000 watts Pep. Which equates to something closer to 500 watts RMS or CW. Just an advertising 'gimick' to make a tuner sound more 'capable' than it really is. If it's done the same way where you are, then a tuner twice as large as you'd think, is about the minimum required. (I love advertising, don't you?)
have fun.
- 'Doc