Ubuntu – External download manager for firefox and chrome

As aria says unrecognized option your aria maybe too old and doesn't support JSON-RPC or RPC at all. See man page by typing man aria2c and search for rpc. In some old version xml RPC is available, but advance features such as pause & resume *adding file* will not available.
Try aria2c --enable-xml-rpc=true for xml rpc. For enabled features: aria2c -v

I'm using JDownloader. However, AFAIK running instance cannot be controlled by command line.

On the other hand, there are add-ons like: - JD Scheduler or - JD RemoteControl

which can do a great job.

See: http://jdownloader.org/home/features http://jdownloader.org/home/addons

(I guess that there will be more tools, maybe someone else will add another suggestion...)