All you have to do is to start JSMS twice and log into each instance of JSMS with the details for each of the two different mobile accounts. If JSMS automatically logs you into the same account both times, then select the "Log Out/Change User..." option from the "File" menu to change the user for that instance of JSMS. Then you can happily use each instance at will.
Note that if you are using the autologin feature of JSMS, it will always automatically login to the last account that you logged into. If you want to get around this you can create two Windows shortcuts to launch JSMS, one for your account and one for your wife's. Then right click on each of the shortcuts, select "Properties", and then the "Shortcut tab" and modify the "Target" field to tell JSMS which account to log in to. What you need to do is to update the target to pass three params to JSMS:
your operator,
your phone number and
your password/pin.
So the target of your shortcut would look like one of the following examples:
"C:\Program Files\JSMS\JSMS.exe" "Meteor.ie Webtext" 0851234567 1234
"C:\Program Files\JSMS\JSMS.exe" "Vodafone.ie Webtext" 0871234567 1234
"C:\Program Files\JSMS\JSMS.exe" "O2.ie Webtext" 0861234567 1234
where 08x1234567 is your phone number and 1234 is your password/PIN.
Note that we store your preferences separately for each login, so you might find it makes it easier to tell the two instances apart by changing the font and/or background colour in each instance. To do that, open the "Preferences..." dialog from the "Tools" menu, go to the "Display" tab, press the "Set fonts & Colours" button and then customize the look and feels of JSMS to your heart's content.