First off, I'd suggest ditching IWP, you are in a new project now and you are thinking about a technology that will have waning and eventually no support in a few years. Custom Web Publishing or FileMaker WebDirect are the alternatives. The former requires web coding experience, the latter requires an upgrade to FMS13 and some other development considerations as well.
As for your relation issue without seeing your file I can't really speculate the cause. Assuming your two files work locally before you upload to Triple8, then all you should need to do is correct the file references to eachother under file > manage > external data sources.
The data source editing window allows for multiple file patsh (one on each line), to correct it, you should use the fully qualified path to your triple8 hosted file, then a second localy path to the file, should look something like:
If the references are correct and you can see all the data from the related file on the layouts in the second file, then you might need to provide more details about the relationship for troubleshooting, (perhaps provide a photo of your relational diagram).
Thanks for your reply and consideration. I will certainly look at the latter 2 web options for future developments. As you have suggested my local reference was not setup correctly. I have fixed this now and the tables are now showing the data as planned. Thanks for your help - much appreciated!