"For their second vote, they choose from a list of the political parties. The remaining 299 seats are then distributed among the parties based on the percentage of votes received nationwide. Only parties that get more than 5% of the vote nationally can send representatives to the parliament."

No. The second vote determines the overall number of seats in parliament that a party receives. Some of these seats are assigned directly based on the first vote. The remaining seats are filled in from lists of candidates that each party selects before the election.

If a party wins more seats through the first vote than it should really have based on the second vote, then that distorts the results of the second vote. Additional seats are created and assigned to the other parties in parliament to restore the proportionality of the seats based on the second vote (or at least reduce the distortion).

Things are a bit more complicated because each party selects a separate list of "fill-in" candidates for each state in which the party runs for parliament. So the national results of the second vote are broken down to the state level, compared to the first vote results of that state, and then "fill-in" candidates are picked for that state. A similar procedure is used for picking candidates for the additional seats that restore the proportionality of the second vote.