Kind of depends on the setup. If all manifolds are up or down (in the basement or above grade) for ease of piping, you could just screw an elbow on the HX then a nipple, union (for future HX cleaning or removal), nipple, ball valve, nipple, air separator with exp tank underneath, nipple, tee, nipple, tee, nipple, tee, with a bushing and boiler drain in the end tee. (supply manifold) For the return manifold same series of nipples and tees without the air separator of course, with just a nipple and ball valve in the tee branches, to isolate the whole loop if needed. In the branch of each supply tee screw a short nipple and then a Honeywell AMX 1" mixing valve, nipple, isolating pump flange, pump, other isolating flange, then out to the system. All nice, neat, and straight. The AMX series cost a little more but they're awesome and save a bunch of money in fittings, not to mention the space savings due to their straight through design. Black pipe is definitely easier to work with, but the looks can leave something to be desired. Copper fittings though, have slop in the cups so unless you're very careful and have a lot of hangers, copper can look awful snaky. Personally I prefer copper most of the time but I also do it every day, and my employer buys the fittings. If you're okay with the look of iron I'd honestly go that route. It keeps itself straight and is a lot easier to fix leaks if there are some as well as add on to in the future if need be, not to mention the cost savings and time spent putting it together.
Do your tubing manifolds have valves and/or drains on them? This would help purge air from all floor loops, but not 100% necessary. I have drawn a rough sketch of what I'd do, but I'll need to log in from my phone to upload it. I did not draw in a Y-strainer, but if you want one (not a bad idea) I would put it in the return main between zone 1 return tee and the ball valve to the left. I would also add a few temperature gauges that I didn't draw in, unless your tubing manifolds have them on which most do. If not, it's not a bad idea to have one on each supply and return so a total of six. I like the Watts temp/pressure combo gauges but if you don't, you'll want 1 pressure gauge somewhere also to keep an eye on system pressure. Between the air separator and expansion tank works well