After you have created a branch and made changes there, you can merge the entire branch back to the main line, essentially replacing the main line contents by the branch contents if the branch line is up to date with the main line. This can be accomplished using the menu item 'Team > Merge changes here...', choosing 'Merge feature branch' and the selecting the branch. This results in merging all changes made on the branch back into the main line.
If this is for some reason not possible and you still want to "overwrite" the main line with your branch, you can just check out both the main line and the branch locally, then overwrite all the files in the main line project directory by those of the branch (except for the
.svn directory) and then commit using the Modeler. Be sure to reopen the main line project in the Modeler after overwriting the files.
In both cases, you will be doing a normal commit on the main line (although there might be lots of changes), so there is no difference in that respect.