Malfoy Manor wasn't the headquarters initially in the 2nd war and presumably not in the first war. Where were the headquarters then?
It’s never mentioned.
There’s never any mention of where the Death Eaters met before they began meeting at Malfoy Manor, or of them having a first headquarters before Malfoy Manor. It’s possible they had one, but where it is isn’t mentioned. Also, it wouldn’t be difficult for the Dark Lord to bring the Death Eaters to a new headquarters, or have their meetings be in in multiple locations, since he can summon them anywhere he needs them without them needing to know the location themselves beforehand.
“There,’ said Snape harshly. ‘There. The Dark Mark. It is not as clear as it was, an hour or so ago, when it burnt black, but you can still see it. Every Death Eater had the sign burnt into him by the Dark Lord. It was a means of distinguishing each other, and his means of summoning us to him. When he touched the Mark of any Death Eater, we were to Disapparate, and Apparate, instantly, at his side.”
- Harry Potter and the Goblet of Fire, Chapter 36 (The Parting of the Ways)
Though it’s never mentioned that the Dark Lord and the Death Eaters had any preferred meeting place during his first rise to power or before he was staying at Malfoy Manor, it’s possible they did and it’s just never said. If there was one, it’d likely be the house of one of the most loyal and wealthy pure-blood Death Eaters, like the Blacks or Lestranges, since it’s unlikely that the Dark Lord himself owned any property and they’d presumably want to meet somewhere they’d have privacy and won’t be eavesdropped on.