My site has a vertical search menu on the left side of the page, similar to Amazon and Etsy desktop versions, with checkboxes and search filter terms. Like these sites, my site automatically performs a search as soon as you check/uncheck an option. There is no extra "Search" or "Go" button. This is great if you only want to choose one search filter, but annoying if you want to choose more than one. In that case, you have to choose the first option, wait for search results, choose the second, wait, etc. (And even more annoying on Amazon where the search filter scrolls to the top each time.) 

How can I make this work great for both the single and multiple filter term cases? I'd be OK with requiring a click on "Go", but not if you have to scroll up (or even move the mouse a lot) to get to it. Maybe some kind of hover "Go" that appears?

Gmail tries to solve this with their label menu. If you click the label's checkbox, then you have to click "Apply" before the change takes effect, allowing you to check/uncheck multiple labels first, but if you click the label name then it takes effect immediately and the menu closes. However, I think this is too confusing. It's really not clear that there are two different actions associated with each row and it took me a while to realize why I sometimes had to click Apply and sometimes didn't. This UI works for the inbox email list where it's clear that checking the checkbox is a different action than clicking the email to open it, but in this case the actions are completely different, not different ways of doing the same thing.