Any plumbing you add will affect flow rates it is just a question of how much. However, I wouldn't expect it be all that much.
As for the cleaner, can you reduce the flow rates from the main drain to help with the suction? Do you have a second skimmer? Sometimes adjustments can be made to compensate and increase suction.
A 1 HP pump should have more than enough suction for a cleaner and everthing else. I run mine off a 1/2 HP pump with 2 skimmers and a MD running as well albeit slightly restricted.
Tell me a little about your setup: Run lengths, pipe size, number of suction ports, return ports, pad equipement, etc. Also, what is the actual pump model you have and what is the running filter pressure with and without the cleaner?