Like you, I make almost everything from scratch and it can indeed be difficult to hunt down all the ingredients in their raw forms. One thing I've noticed over the years of using FitDay as well as the USDA's National Nutrient Database (which functions similarly to FitDay) is that you sometimes have to search for a raw food in its plural form if the singular doesn't work at first, or vice-versa.
So, when I search APPLES in FitDay all kinds of processed food appears, but a search for APPLE comes up with the raw food at the top of the list. Similarly, the USDA's database comes up with all kinds of crazy food-like substances when I search for STRAWBERRY, but a search for STRAWBERRIES produces the real deal.
If all else fails, I highly recommend using the "Browse" function until you are super familiar with how this site works. However, there are a few examples when combining "Browse" with "Search" is your best option on FitDay. Try browsing through FRUIT & JUICE-->BERRIES, for example. You'll find there is no selection for STRAWBERRIES, RAW, but a search for STRAWBERRIES will work. In other words, have patience and give yourself some time to figure out the site's quirks.
I also recommend checking nutrient values against the USDA database if you are unsure whether or not you've selected a food in its raw form. It is also fascinating to see the nutrient values for foods in super "high-def", if you're into that sort of thing anyway. Here's the link to the database http://www.nal.usda.gov/fnic/foodcomp/search/
(hopefully not a problem to post this since it is USDA research, not a competing site -- I think FitDay uses the same data for many foods).
Hopefully that helps! Happy logging!