How to understand the meaning of each column in "site window" and "link window"?
In multiple site link popularity mode, "Hits" column of "site window" is the number of found web pages who linked to this site, duplicate records returned by multiple search engines have been skipped during calculation process. "Hits" column of "link window" is the number of sites who has been linked by found webpage address (first column). Other every column of "link window" means whether this webpage address has link pointed to correspondent site or not.

In single site link popularity mode, "Hits" column of "site window" is the number of search engine query result records, duplicate records returned by multiple search engines have not been skipped during calculation process. "Hits" column of "link window" is the number of search engines who includes found webpage address (first column) within its query result. Other every column of "link window" means the ranking of this webpage address within search engine query result.

I just subscribe to daily expired domain lists and need a software that can tell me the link popularity of thousands of domains at once. So is it possible to import domains from a .txt file with Link Survey?
This kind of task is not fit for Link Survey. By design, Link Survey should be used to find out every inbound link to a website, so that it will take long time to figure out the total number of all inbound links. If you just need to know the total number of links to evaluate the value of some deleted domains, you may try our another software product Domain Inspect instead, which can be found at here.