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Sorry if this is a really stupid question but I am an absolute beginner so can anyone tell me how to work out in what order the strings should hang to start the multi coloured alpha patterns so the pattern comes out right?

This is not a stupid question. Problem is that there's no real answer as there are different methods to do a multicolor alpha.

Have you already had a look at the tutorials? There's one that explains most methods, and they show what you can do, like use multiple strings as one or only add a string when needed.

On the other hand I'd never suggest to do multicolor alphas for a beginner. They are really hard to do, you need a lot of experience. You need to know how you vary the thickness of your knots or to switch strings, how to add new ones in a way that's not visible, how to hold strings, especially as they have to be really long, how to measure the length of your strings and so on.
I'd call myself an advanced knotter when it comes to standard style bracelets, but even two color alphas are a totally different thing.

Rissa has a point. See for me right now my base strings are always the same colour and all the colour switches are done with background strings. However, not a lot of people do it the same way.

The best thing I can suggest is check out the tutorial and just experiment with smaller designs just until you figure out which method works the best for you :D