It's not clear, but I think most people would assume that in both cases, the adverb modifies both verbs.
If you want to make the adverb modify only one of the verbs, you can change the word order:
"They ran and quickly jumped."
"They ran quickly and jumped."
More subtly, you can use punctuation:
"They ran, and jumped quickly."
"They quickly ran, and jumped."
If you want to make absolute certain that the adverb modifies both verbs, you can turn it into a sentence adverb:
"Quickly, they ran and jumped."