You can use an svn changelist to keep track of a set of files that you want to commit together.
The linked page goes into lots of details, but here’s an executive summary example:
$ svn changelist my-changelist mydir/dir1/file1.c mydir/dir2/myfile1.h
$ svn changelist my-changelist mydir/dir3/myfile3.c etc.
... (add all the files you want to commit together at your own rate)
$ svn commit -m"log msg" --changelist my-changelist