It's easy to configure Chrome to use Tor to preserve a semblance of privacy online (http://verahill.blogspot.com.au/2013/06/450-tor-and-chrome-on-debian.html). There are a few, simple things you can do to make your life with a proxy easier to manage.
This post presumes that you've followed this post first: http://verahill.blogspot.com.au/2013/06/450-tor-and-chrome-on-debian.html. In particular, that you have turned off pre-fetching.
In addition, you may want to think about the following:
On the lower end of the scale, you may or may not want to use incognito mode consistently. This has little bearing on privacy online, but it depends on whether you want to leave traces on your computer of your browsing history. Although that should only be an issue if someone gets physical access to your computer, you never know if the next browser bug will give someone complete access to your history. Most likely it'll only provide metadata (which is what the NSA brouhaha has been mostly about).
Anyway, if you feel this is an important issue then you should probably be encrypting your disks with encfs as well.
It's probably more important to rethink how you are using search engines in Chrome. First of all, you should turn off instant search. Secondly, you will want to consider whether you want to use google as the default search engine for queries in the URL field. Two main search engines come to mind: duckduckgo.com, and startpage.com. While duckduckgo.com has a higher profile, startpage.com is a bit more full-featured, and that's because it takes your query, anonymizes it, and passes it on to google. It's also based in Europe, which I (probably naively) feel is safer.
Go to startpage.com, and click on 'add to chrome' under the search box. Then set Startpage HTTPS as the default in Chrome:
Also consider making sure that google.com isn't your home page in chrome.
Even though Tor works fine in general, it can be a bit slow, and you don't want to use it for everything anyway. There are times when you don't want to use a proxy. In my case, that's when I visit journal websites or my university websites. Also, I have set up a reverse proxy via my home router, and it's faster than Tor, so for a lot of things I'm fine with using that.
Switch ProxySharp supports the creation of rule-based proxy switching. In my case, I've set it so that if I use google, I use Tor. If I go to RSC, ACS, Wiley or Elsevier journals, I use my university connection, and for everything else, I use my home router.
You then just need to click your way through to the proxyswitcher alternative: