Are you sure you want to put the two manifolds in parallel with each other and separate the returns?
If you run them in series and use closely spaced tees for the supply and return lines of each zone, the system will balance quite nicely and be easy to handle high and low demand times of all the zones.
It can also help your boiler maintain a steady temp, with a constantly circulating primary loop.
If you are going to have a circulator pump in each zone, it gets even easier. One Tstat for each zone/pump, the closely spaced Tees takes care of the rest.
As for the primary pump placement, with the above system, I prefer to pump INTO the largest resistance. If you use a continuous primary loop, your Boiler is the biggest resistance and you can put your pump at your boiler to pump INTO the boiler. This is the method in a number of Installation Manuals for boilers.
The individual zone circulators + closely spaced tees would take care of balancing its own zone with the rest of the system.
How many radiators are you expecting to have on each zone?
Split Tee design for supply and return lines of each zone, with a balancing valve (ball valve), one on each side to account for different resistance of the radiators, etc. You can even mix radiators and baseboard, or whatever in this setup, it doesn't care
Split Tees will help keep more of your radiant elements (rads/bb) at the system supply temperature, thereby improving (sometimes significantly) how well they provide heat to the zone.
125' plus radiators could be a SIGNIFICANT resistance. Balancing the separate manifolds and individual zones could be a bit of a challenge without zone circulators and such.
FWIW, "pumping away" is pitched as the "ideal" way to plumb heating, but a lot of things have to be right and all has to match up. If done right, it's good. The way I mentioned above is pretty forgiving- both of mistakes and compromises due to location, walls, pipes, etc.
Edit: Here's a link to my system, using closely spaced Tees and backup oil boiler. http://nepacrossroads.com/post554753.html?hilit=system%20diagram#p554753