First, you need to make sure you're working on the correct branch
before you make changes. You can switch between branches by
right-clicking on the project in the left-hand panel and selecting
Replace With > Another Branch or Version. This will show any branches
you've created, plus the main HEAD branch. The project's icon should
show the name of the current branch, if one other than HEAD has been
selected.

Once you have the branch checked out, you can synchronize with it as
usual to check your modifications in and out. You can also switch
between branches as often as you'd like, but make sure all your changes
are committed first or they'll be overwritten.

When you're ready to merge changes from one branch to another, first
switch to the target branch -- the one you're merging into. Then
right-click on the project, select Team > Merge, and input the name of
the branch and its starting tag. You'll need to resolve any conflicts
by using the Synchronize view.

The Eclipse documentation has a lot of useful information on working
with CVS, by the way; it's in the Workbench User Guide. Hope this
helps!

-- David