From here, it's best to create your own branch. This will ensure that any changes you make are to your own branch, and you do not edit the files in the main UNIFIED branch. So if you make a mistake, you don't need to clone the entire repository again, you can just update the unified branch to HEAD, create a new branch, and continue just like you are editing a fresh repo.
See this post by dmilligan:
http://www.magiclantern.fm/forum/index.php?topic=9524.0
- Select the commit panel
- Click on Branch: default
- Select Open a new named branch, and give your branch a name
Lets commit the changes.

- Enter a commit message
- Hit the commit button
- Create branch
Note: You can edit files before creating a branch. This way your commit log doesn't contain a commit solely just for a new branch. Instead, the new branch will be created as you commit your changes.
The changes are reflected in the commit log.

Lets merge some of the other branches with our local repo. For this tutorial, I'll be working with the 5D3.123 branch.

- Scroll* through the commit log and find the first entry for the branch
- Right click on the commit and select Merge with Local...
* Or as a1ex points out below, you can select the loupe which opens the filter toolbar.

- The loupe
- Filter by changeset type
- Filter by branch
A quick summary appears, click next*

* Enabling the option to automatically resolve merge conflicts seems to fix some weird conflict messages.

And a summary of the merge.

There are some conflicts between the branch we are merging (5D3.123) and the local repository. Click on the
resolved.
Here we have a summary of the conflicting files.

With all files selected, lets click Tool Resolve.
This moves the files to the Resolved conflicts panel, and we can resolve each file.

Select a file to resolve, and select Diff to other.
This will automatically open the Meld diff tool.

From the changes menu (
1), you can push and pull changes as needed.
If there are other conflicts in the file, you can select the down arrow (
2) which will show you the next conflict in the file.
After all conflicts have been resolved, you might be greeted with this.

Success!
Click save (
3) and close Meld.
When you have resolved all conflicts, click close.

This takes us back to the merge summary, and we can now click next.
We end up at the commit summary.

We can change the commit message if wanted, and click commit.
A final summary appears, we can click finish.
The result is reflected in the commit log.
