I figured out how to make the second weather tab work with another theme. If anyone is interested this is how I did it. I'm sure there is an easier way but this worked for me.
1) Back up current theme in M2DC.
2)
a- With total commander go into windows>themes you will find the backup you just made and rename it to "originalbackup"
b- (optional) copy originalbackup.m2dct and go into program files and create a folder called M2DC. Now put all your .m2dct themes in this folder and when you have time direct M2DC to that folder to add all the themes in it. This just keeps things clean.
3) Go into settings>today and disable touchflo.
4) Take new theme files and put them in the windows folder or the m2dct and put that into the new M2DC folder you created.
5) Go into settings>today and turn touchflo back on. (now when you go back to your home screen some of the tabs will be messed up. This is ok for now.
6) Go into M2DC and create a back up of the current theme (the new one loaded)
7) Now go into M2DC and add the originalbackup.m2dct and apply it. (You will now notice your second weather tab is not there)
Reboot
9) Go into settings>today and disable touchflo.
10) Take attached HTCHomeSettings.xml and put it into your windows foler. You may have to overwrite the original.
11) Go into settings>today and turn touchflo back on.
12) Reboot
13) Back into M2DC and choose the backup of the newer theme and hit apply.
You should now have your new theme with the second weather tab
In my theme to make things cleaner I copied-
hh_fw_bigicon_weather
hh_fw_tabbg_weather
hh_fw_tabicon_weather
Then I added a 2 to look like
hh_fw_tabicon_weather2.png
Disable touchflo again and copy those three files to the windows folder and now they all look uniform
I am using this theme
here.. Here are some screenshots. This whole thing was much easier than it seems