In order to create a SpecMol reource, you need the molecule in a structure file (like mol, cml ...). You also can include one or more existng spectra. Choose "File" -> "New" -> "SpecMol" -> "new SpecMol". You first need to choose a name for the new smr file, then the molecule you want to include. On the next page, you can choose the spectra to include (you need to select them in the file tree view and then pres "Add spectrum" to include them). If you do not include a spectrum, an empty one will be created. After you hit "Finish", the resource will created and show up in the Bioclipse resource view. It can be opened e. g. by editing in the SpecMol editor.
You can also add an existing spectrum to an existing SpecMol resource. Right clicking on a SpecMol resource gives the menu item "Add a spectrum to this SpecMolResource", which gives you a dialog to choose spectra. This spectra will be included in the SpecMol resource.