A lot depends on how many courses you need to move. If you are replicating a site and have access to the server, then it is better to do an entire site backup (database, moodledata, moodle code) and install that on the new server.
Another option is to increase the maximum filesize for upload, http://docs.moodle.org/22/en/File_upload_size
However, I sense you might want to copy just a few courses. Here are some tips:
- When you backup courses on the first site, include only the data you need. Do not include course logs. Do not include grade history or enrolled users if you do not need that information.
- If the backup files are still too large after excluding the data mentioned in #1, then backup a few segments at a time - these are selected on the second page of the backup process (on later versions of Moodle). This means you will have multiple backup files for each course. Backup file #1 might have the General and Segment 1 areas. Backup file #2 might have Segment 2 and Segment 3. And so on.
- Look for large content files, such as videos, that you might have uploaded into your courses. If it is possible to later add those to your new courses, create backups that exclude those large files. Then upload those files to the new courses. In general, I recommend keeping large video and multimedia files hosted outside Moodle.