Well, what you suffer is lack of experience (with no offense). Personally, I jumped into it and have been learning ever since (that is since 1998). There are a lot of things you just know over time, but with each project there are new obstacles to master.
One of the things that help a lot is looking at queries when you use phpMyAdmin. You can figure out a lot from there. After a while you get around to the client since it's faster than all the clicking, but there is nothing wrong with frontends to begin with. Also, I'd seriously recommend learning what the different indexes do and what each is used for, then develop a habit of running EXPLAIN on your statements (often) and go from there.
I know it sounds super cheesy and elitist, but the MySQL manual is a really great resource. Chances are you will work with technologies/languages where the documentation really blows and you will look back and know what I mean.
Reasons as of why the manual is awesome are, they explain everything and they also do it really well. On top of that, the manual also has comments on each page which provide a couple pointers where the manual left off to early (doesn't happen often, IMHO).
In the beginning my other favorite resources to learn used to be Devshed and Sitepoint, but I haven't been there in a long while. Read the tutorials (even e.g. when you are not building what they are building, just look at the code). Last I remember, they also offered pretty active forums/communities with a lot of knowledgable people.
And then, there's always opensource. Use the force, read source. If you are using an app and they do something and you want to figure out how they did, read the source and learn from it.
As for books, all the cookbooks are pretty good. In general I recommend all the books with an animal on the cover (O'Reilly). They have never let me down.