Emacs Magit issue with Git Wrapper

Question

In my daily work I have to use Git. I have been using Emacs and presently wish to use the Magit package.

The problem is the Git program in my work flow has a wrapper (let's call it as myGit) over it to customize a few functions (most of them are exactly same as for Git).

I have tried aliasing git to myGit but some operations (like pull) don't complete successfully. For example, from shell we issue myGit pull . for pull operations and myGit pull -s . when there are local staged/un-staged changes. Internally, it invokes git with appropriate args (like rebase, merge, etc.) to complete the operation.

Two questions:

1. How do I ask Magit to use myGit instead of git (aliasing might not be the most elegant way)?
2. How do I override pull and a few other operations with those which are done through shell for the wrapper?

(While trying to use Magit with Emacs, normal pull operation isn't completing properly. It shows unmerged files with origin.)