Are you filing discretely (one at a time) or batch?
If you are filing discretely, you would fix the errors, and file again. On the 'cover sheet' of the adobe file, you would select "Amendment" instead of "New" for SUBMISSION TYPE, and you would include the DCC number you recieved from the acknowledgement in the box below.
If you are a batch filer, and you are using some kind of software to generate the batch files, you should contact your vendor for guidance on how to deal with tracking and amending CTRs with errors.
You _can_ file a discrete amendment to a CTR that was originally filed as part of a batch, but I believe I recall reading that they prefer the types remain consistent. I can't seem to find where I read that now, though, so I may be incorrect...