You should search this site as I posted one on this topic.
The gist of it is that you can use this dos command in a batch file to co:
FOR /F "delims=" %%i in ('dir /s /b') do cleartool co -nc "%%i"
to ci a little more involved but not bad:
@echo off
if "%1" == "" goto END:
FOR /F "delims=" %%i in ('dir /s /b') do cleartool ci -c %1 -nwa -ide "%%i"
goto DONE:
:END
echo usage: ci p1
echo where p1 is the tagging label for the checkin
:DONE
(the above commands don't work at the dos prompt as you must use % instead of %%. Also, you must manually "add to source" and rmname any files that you decide to add, move or remove, say, in the setup files pane dirs, etc.)
I suggest that you leave the entire project checked out when building and making changes. When done working, ci. Before building, co. Reason is that IS changes files in multiple places and for you to catch them all is a chore.
You should be working out of a single branch anyway. Although, we are allowed to change the trunk uptil a point (release candidate). So I am unsure what all your problems and the solutions may be.
If you have specific questions, use the this board's messaging and I'll see if I can help.