Anonymous
For the IP phone on remote side to really recognize
Ehh with remote side you mean a phone connected to the LinkSYS or D-Link. I hope you do not mean a phone connected on another site.
If so you have to introduce VPN, that is really the only way to go about having phones connected as an extension from a remote site into your site. That will involve changes on your modem.
That process is messy and you have to do some serious reading up on that because if you get lost in it you can bring your network down.
The 5060 ports are for SIP traffic so I would recommend to use them for that. To manage the 3cx Server remote, yep you can do that but you have to setup a virtual server for the 3cx admin console. In your case you have to add port 5481 the same way you added the ports for 3cx.
That should work.