Networking is both fun and hard work.
Here are some resources that can guide you.
PAC Manager has a solid chapter on assigning network addresses to both Ethernet ports;
Likewise the PAC S Series Controller Users Guide has a good section on laying out networks and using both ports (applies equally to PAC R controllers); http://www.opto22.com/site/documents/doc_drilldown.aspx?aid=2668
The PAC System Specification Guide also has as chapter on Ethernet configurations;
Lastly we have an entire doc on networking Opto 22 products;
Bottom line, as you know, you can assign a different address to each Ethernet port on our R and S series controllers, the only proviso is that they MUST be on different subnets.
After that, you are at the mercy of the network admins.
Lots of customers use the two ports, its pretty common, its not hard, it just requires clear diagrams and communications with the network guys so everyone knows whats needed.
George has spot on help with the advice that you can only have one gateway configured.
The ship to shore stuff sounds interesting.
Not sure there is enough information to hit it, but lets take a swing......
I'm assuming that along with SoftPAC on the ship, you also have PAC Display running because you say that you want the ship trend data to show up on the shore PAC Display when it gets back to the dock.
In this case, I would install DropBox on the ship PC and set the sync folder to be the ships PAC Display trend directory (PAC Display config can set where the trend files will be saved).
Each ship should have a suitably named directory (different for each ship) so that the trend files do not get mashed on the shore PAC Display.
Once each ship gets back to doc, DropBox will sync the trend files and they will show up as history files on your shore PAC Display.
If you want to be notified when the ship gets back, I would use the I/O enabler chart.
Its included with your instillation of PAC Project on your hard drive (or you can download it from the 'Samples and Freeware' section of the website; http://www.opto22.com/site/downloads/dl_drilldown.aspx?aid=3604 )
As it stands, it inserts a message in the R1 error queue, I would tweak this part of the code and not put it there, I would rather make a variable that pops up a message on the shore PAC Display, or have the R1 controller send an email or text.... what ever notification works for you.
(Hint, set the ship SoftPAC as a 'Generic MMP device' in the 'I/O' tree off the R1 so it can poll each ships SoftPAC controller as if its I/O).
If I misunderstand and you don't have PAC Display running on the ship, just SoftPAC, then you must be logging the temperature in a local file.
You need to FTP that file from the ship PC to the shore PC when it gets back.
You could add the File FTP example (also on your hard drive - or download from here; http://www.opto22.com/site/downloads/dl_drilldown.aspx?aid=4217 )
This could be linked in with the I/O enabler chart.
Or, you could have a batch file on the windows PC to FTP the data over (using something like Filezilla) when it connects to the dock WiFi network.
In this case, you will need to either store the data on the ship in a format that PAC Display can read, or use another bit of software to read the data file (something like Google Docs or Excel).
Hopefully some others chime in with some ideas of how all this might work for them.
None, the less, I think between what George pointed out and some crazy brain storming ideas here, you can take another look at things.