I use down and flat for Katie. Down is the legs in front, ready to go again, easy to get up from and flat is laid on her side. I used to use the 2 different words on my collie who I worked obedience with. I used to tell the dog down and then roll her onto her side saying 'flat'. I used to lay her like that for the down stay in obedience comps as it was more difficult for her to get up from that position. When I got Katie I automatically started to use the command and laying her on her side, and considering she's stubborn sometimes she got it pretty quickly, another way of teaching something like that is to wait till the dog does it natually and say the command although this may take longer for the dog to understand the actual command.

Thanks for the advice Katherna, as we already use 'down' for your 'flat' I'm gonna try 'drop' for your 'down'. Have figured out if OH and I throw the ball to each other she gives up trying to catch it and waits in the 'drop' position (crouched), so everytime she does this I use the clicker and say drop, then reward. Will have to wait and see if this works!

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Fingers crossed for you

Just tell the instructor, that is the down you like.

I agree with Nanna - at this stage the focus should be on socialising, focussing, and basic commands. Just pick the command/position you like best, and until and if you are ready to move onwards and upwards you can progress with the finer points. I have seen a lot of this, the instructor might have an eclectic mix of types/abilities/ages, but all he/she wants to do is get to the finer points, as if everyone wants to enter comps. Most people at that stage just want the basics.

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It only takes a minute to find a special one, an hour to appreciate them, a day to love them, and a lifetime to forget them.

But your only at Puppy Class at the moment, so for the time being it shouldn't matter, I think it's a bit cheeky that they made you embarrassed over it, your instructor should be glad that your puppy can do that.
With my Golden Retriever, Bobby Dazzler, I find that he learns quickly when I show him what I want him to do, so for example put your pup in the down position, then put her in the position and say the command (what ever you choose) then praise, keep repeating, giving lots of encouragement. Don't do it for too long because they'll lose concentration, but make it a really fun task for her. Always end on a positive.

If she's a border collie, she'll get it in no time!