Define the directory structure first, then create and use the download description file:
aria2c -i uri.txt
where uri.txtmay contain
http://serverA/file1.iso http://mirror-serverB/file1.iso
dir=/downloads/a
out=file1.iso
http://serverA/file2.iso http://mirror-serverB/file2.iso
dir=/downloads/b
out=file2.iso
Keep in mind that aria2 is a download utility, not a synchronization like rsync or lftp.
Link to the answer rsync: fooobar.com/questions/1572944 / ...
and the lftpanswer: https://superuser.com/a/305236 .
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