I have Elder and Count, and two other cards. I use Elder to play Count. According to Elder's ability, I get to choose two, not one. I'd like to topdeck a card and discard one. But when I choose the topdecking effect and the discarding effect, the discarding effect triggers first, discarding both of my cards. Instead, I should choose the order of effects, and then I can choose to topdeck first.
That's correct behaviour, you don't get to choose the order those effects happen. That's isn't special to Elder, all the cards that give you (at least potentially) more than 1 choice have you do the effects in the order listed on the card. For Elder, that rule still applies.
For example, if you Scrap a card costing $2, you can choose "+1 Card" and "gain a Horse" as the 2 effects. But you have to do them in that order, meaning that if your deck is currently empty, you draw a card (including shuffling the discard pile) before you gain the Horse (meaning it misses that shuffle).