A whiteboard. Seriously. You MUST draw out organic chemistry to understand it. The second part of Organic I at my school was just a TON of reactions. They are not hard, there is just a lot of them. Practice, practice, practice. It takes time to get it all down. Mechanisms will you help you understand why and how reactions work, but they take time. Recognizing what you can do with functional groups is essential. Currently, I'm in organic II, so hopefully what follows helps a bit. I'm not trying to impress you with my knowledge, I'm just trying to get you to understand the thought process.
One exercise that is very useful is to start off by thinking of a molecule, with a whiteboard in front of you. Usually I just start drawing carbon chains or rings and then add a function group, and then pick a product I want to achieve that has an attainable functional group. Take for instance benzoic acid, let's make that our product. How can we make benzoic acid using anything we need? Let's start close to home with benzaldehyde. We need to take this aldehyde to a carboxylic acid. What process does benzaldehyde need to undergo to gain an oxygen/alcohol? What converts an aldehyde to a carboxylic acid? A strong oxidizing agent should do the trick. Potassium permanganate in water will take you to benzoic acid.
Now, exercise a different way you could get to benzoic acid. This time, start with just benzene. Friedel-crafts acylation with formyl chloride in aluminum chloride can take you to benzaldehyde, and now you can just use the oxidizing step you used before. You could have also use Friedel-crafts alkylation with methyl bromide in aluminum chloride to get toluene, and then use a strong oxidizing agent again. Benzoic acid results. These two methods are similar, but you just used your knowledge of A.) nomenclature (structure from name), B.) Aromatic reactions (F-C Alk, acyl), and C.) Oxidation.
If you can, try to always name your reagents and products. My instructor always put stuff in words on the exam so it could get pretty scary if you could only recognize structures but not names. This tripped up quite a few people in my class. Now, back to the reaction.
What's another way I can get benzoic acid? Well, let's say I had only carbon dioxide as my initial source of carbon. I know I'm going to need to add that benzene ring somehow. I recognize that there is two oxygens in CO2, and my product also has 2 oxygens. CO2 also has one carbon, so I need to add 6 carbons to get to my product. How can I do it? Well, with the grignard reaction I can add phenylmagnesium bromide in ether to get me to benzylate ion, which I can then give an acid to bring me to benzoic acid. Try to understand what exactly is happening in the grignard reaction. It's a carbanion attacking a carbonyl. Practice moving the carbanion electrons to the carbonyl, and then pushing the bonding electrons (otherwise our octet would be broken) up to the oxygen to give us the ion. Practice moving the electrons from the benzylate ion's oxygen to go grab the extra proton off the acid.
This is how I think when I practice reactions. Retrosynthetic analysis, as my professor calls it, requires you to know everything about the reaction. There are many pathways in organic that can achieve the same result (on paper). When you repeatedly practice these pathways, synthesis problems on an exam will be easy because you have so many different ways you can utilize functional groups. I did something like 12 steps for a 3 step problem on my second organic exam and got full credit (and a 100 overall). Now obviously if a question says use 3 steps, you use 3 steps. But, you have to build this toolbox that allows you to have as many options as possible so you have access to those exact 3 steps.
Hope this helps, and my apologies if you haven't covered the reactions I mentioned. This was the material that was covered around this time in the semester for my organic I.
