What are main methods for econometrics of Macroeconomics?
There are many different econometric methods used in macroeconometrics, but the basic ones are advanced versions of least squares methods and Generalized Method of Moments (GMM). Structural VARs, ARCH/GARCH models and several others are widely used as well.

Since you're already familiar with econometric methods, you might try glancing through Fair's "Macroeconometric Modeling" (http://fairmodel.econ.yale.edu/mmm2/mm.pdf). You don't necessarily have to read it completely, but I found it a really useful document in understanding how to build and use macroeconometric models.

Based on your background and interest, I'd recommend Favero's "Applied Macroeconometrics" and De Jong's and Chetan's "Structural Macroeconometrics" as general books on the subject.