No need to uninstall the Cydia version.

iFile is probably the easiest way to install the .deb. If you copy the .deb to any directory on the phone you can browse there with iFile and just touch and install it.
You can even put it on the iPhone with iFile. You just browse to the folder you want to drop the .deb in iFile and hit the Wifi looking button on the bottom. Then it will tell you the IP of your phone and port 8080. Just browse there with your desktop on the same wifi network and you can upload the .deb.
Other options would be to use sftp to copy the file over and from the command line run "dpkg -i Todo*.deb" to install it.