Here are a couple other ideas you might find useful:
If you have JS Bach's Cathedral, build size 2 cities that maximize production (ideally, build on a hill that you have started to mine, and that has access to 2 other hills; forests are a substitute if you don't have enough hills). These cities can have as many units outside the city as they want, because Bach's will make all citizens content.
Try setting up your civ in such a way that you can counterattack rather than trying to defend every city. Large cities and guerrilla warfare can help, since your enemy will be forced to deal with partisans (either wasting movement points to stop them from appearing, or attacking them after they have arrived) rather than continuing to advance forward. In most circumstances, attacking units will have an advantage over defending units, so attacking is preferable to defending. In fact, the best way to counterattack is to bribe your city back; captured cities will be in disorder, and the fact that they were previously yours means that you can bribe them back for 25% of the normal cost, and get whatever units are inside the city and next to it as well. The downside is they will get a technology when they take a city.
To minimize your vulnerability, you'll have to plan your rail network carefully, to prevent losing too many cities in the initial attack. You may want to make your rail cross hills or mountains that you can heavily defend (a small city with walls, barracks and a few vet defenders, or vet defenders in a fortress). If you can't do that, have size 1 cities with a defender, but no walls, in place, so that in the event of invasion, if the city is destroyed, the rail connection is broken. Just keep enough engineers "on call" (engineers that are either pre-charged, or have actually finished a job, so that you don't find that all your engineers have "moved" before you can deploy them to fix your rails) to actually build a rail, or to build a city there to have the exact purpose as the one just lost.
The only effective counter to this strategy I can think of is to bring in enough engineers to "fix" your network, or build around choke points. Of course, this means that they will have to reduce their army size in order to have enough engineers. Engineers are much more costly for Fundy (and Commie) civs than for democracies because of their lack of WLTPD. Also, they need their engineers back home to irrigate the land in order to grow at a decent rate. Moreover, bringing engineers into a war zone means they have to be defended, or they stand a high risk of being killed. Partisans gobble up undefended engineers because they get a x8 attack bonus against units with 0 attack. If you keep a few near places where you expect your opponent to build roads and rails, you can punish them severely for their actions (kill 2-3 engineers) if they don't think to leave a military unit behind.
This brings up the last tip:
Any partisans supported by a city that starves to death will not be disbanded, but become NON units instead. So, if you want to scatter partisans around your countryside (or around your enemy's countryside, for that matter) you can do this without having to suffer unhappiness.