The '90 days' means 'up to 90 days' and can only occur in one lump period of time
That's not quite true - it's 90 days in any period of 180 days, so if you go out of Schengen after say, 80 days spent there in one go, you still have 10 days left.
But I will still have a few days left on my 90 days when I return - is this really necessary?
The ultimate decision whether to let someone in or not lies with the immigration people at the border. Personally I'd rather have all the documentation with me that I can think of if there was a lot riding on my being let back into the country, but it's up to you. Now I'm thinking about it, I'd also ask for the mobile phone number of the official who gave you this advice... (yes, I know, I'm beginning to sound paranoid, but I've lost count of the number of times I've been given one piece of advice by an official that counts for nothing with another).