There is one book that will perfectly suits your needs:
A biologist's guide to Mathematical Modeling in Ecology and Evolution, by Sally Otto
It is a very good book that is very easy to understand and in the meantime goes pretty far (It ends with the use of diffusion equation in Evolutionary Biology). I highly recommend it.
- How to create a model
- Function approximation
- Find general solution with $n$ variables for discrete and continuous model
- Stability analysis
- Find equilibrium
- Analyzing cyclic behavior
- Gives very good introduction in linear algebra and probability theory
- Class structured population
- Stochastic modeling (birth-death processes and diffusion approximations)
- All examples are from the field of ecology and evolution and the author derives many of the most important equations in ecology and evolution.
Also I think that Khan Academy is a very good and easy source of information for improving your math skills but it takes quite a bit of time to go through all these lectures.
For a good and complete introduction to probability theory, I'd recommend this MIT Opencourseware but again, it takes time to go through all these videos.
For further recommendations in population genetics, you should have a look to this post.
If you are interested in theoretical biology, you may also want to learn about programming (if you don't already know much about it). $R$ is used for data analysis purposes, $Mathematica$ or $Matlab$ for deal with mathematical modeling and $Python$, $Java$ or $C++$ for individual-based simulations.
Note: A bit less than 2 years ago, I had the same interests than you and had to face the same issues than you.