To answer your questions:

1. There is a national list for each party for the 2nd chamber elections. They do list where the candidate comes from on the entries, and some parties do make an effort to get a spread of candidates around the country, but there are no local lists for the national elections.

2. They can be elected directly if they get enough votes.  The formula is as follows: from the total number of votes, the number of votes for one seat is computed by dividing the total number of votes by 150 (it is called the "kiesdeler"). If the number of people voting specifically for you is more than 25% of that number, you're in. I believe this number has been changed a few times, but I'd need to look that up.

3. There is no threshold.

It is possible to get just a single seat through the elections, but currently the only single seat occupants are the ones who split from their parties (Wilders and Lazrak).