Begin by writing an introduction that lists the states you wish to compare. In the introduction you will also want to make mention of your variables. If you are, for example, comparing food policy in Germany and Denmark, you will want to briefly touch on what makes those two countries comparable in all but one key area --- that area should be food policy. In other words, you want to explain to the reader that Germany and Denmark are virtually identical, except for this one aspect, about which you plan to write.
Write your rationale with your argument arranged by topic, not by state. That is to say, don't write a section about one country's policy, followed by a section about the other's. Cover each policy, touching on each state, with every paragraph or every other paragraph containing references to all the states you wish to compare. This leads to a more naturally flowing article, and will lead to a more tightly formed argument.
Cover all your bases. If one state is much larger than the other, explain why that difference is not important to the research you hope to carry out. When someone reads your rationale, he should be able to glean an accurate picture of why you chose to compare the states you compared. He should also get the sense that you have controlled for all the variables involved in the topic you are covering.
Admit your limitations, and the limitations of the study. No study is perfect, and no professor is expecting your research to be flawless. Concede the limitations to your study, and feel free to elucidate scenarios in which your conclusion may be mistaken altogether. If you have clearly explained how you carried out your research, you should feel comfortable defining areas where you found existing statistics or general information lacking, and perhaps even conclude with potential avenues for future researchers.