I hooked up a Honeywell RTH6500 stat to a Taco boiler pump control, a 2 wire system. It also will work for a Honeywell TH6000 series wifi stat. This only works to control the boiler pumps only - no A/C. The boiler pump control has no C terminal. I use the Rc and C terminals on the stat to power to stat. R and W to signal the pump relay.
This is what I did. Ran new cable. Replaced the old 2 conductor wire with 5 conductor (using 4 wires). Remove the Rc/R jumper on the stat (important!). Connect Yellow to Rc and Blue to C. Yellow will carry power. Blue is common. Connect Red to R and White to W. This will switch the pump relay. At the boiler control install a 110v to 24-28 v transformer. The transformer is not switched with the boiler so the stat stays on oven when the boiler is turned off. Connect the R and W conductors to the pump relay terminals. Connect the Y to the transformer 24v hot terminal (usually labeled R). Connect the B to the other (common) transformer terminal.
On the stat setup you need to identify the system type as heat only without A/C (system type 2 on my Honeywell stat). This worked in my case because I could run new wire and didn't need the A/C control. My problem was at the pump control panel and a second transformer to the A/C side of the stat solved the problem.