I am in pretty much the same situation as you; however I have 5 builders and plan my upgrades in advance so every evening I have at least 1 builder finish an upgrade. I go online, boost 1 barracks and raid with Barch/gobs to get the loot I need to do my upgrade(s) for the evening. I stay on constantly for the 2-hour boost and can almost always grab the 1-2 million of whatever resource I was looking for. Then, before I start my upgrade I dump the extra into walls (though that will be harder soon as I only have a few lv 6 walls to upgrade), then start my upgrade(s) and log off with less than 1 million in my storages.
I rarely get hit with a large raid, mostly TH snipes, and the ones that do are usually revenges from people who I robbed earlier. But even a full-on 100% only gets them less than 150k of each. The only thing I hate is to see that they got any of my DE...





