when I enter the word I am reading into a dictionary
I think this might be the step that's getting you. I would first and foremost recommend a paper dictionary, but if that's not possible, I'd recommend an online dictionary you can "scroll" through.
Take for example Lewis' An Elementary Latin Dictionary. Here you'll see the whole dictionary divided first by initial letter, than in groups of words, then finally individual words. If you're unsure of the nominative of a word, getting as close as possible to the root means you'll either eventually stumble upon the word or a related word that provides you that base word. It's easier to do this with a paper dictionary, so that's why I suggested it as my first choice.
Where things can get tricky is if the oblique form and the nominative are very different, you'll sometimes have to spend an inordinate amount of time looking. Like, say, you have agris, and you don't know the nominative. In cases like these, one online tool is a morphological parser, such as the one by Perseus. You type in the word, and it gives you all possibilities of what that word could be.
Of course, after a while, as you learn words, you'll just remember them. And there are patterns of inflection. So learning your case endings and several hints as to what, e.g., the third declension does in oblique cases will help you recognize the words on sight.