Unfortunately, based on the very little information provided I can't give you much... There are some basic rules used to calculate the water heater's horizontal vent connector length (general advice is: as short as possible), and a few reasons that might be causing the WH's pilot to go out.
I've answered similar "pilot going out" question a few times, just follow the links below:
Going back to the vent connector and "how much is too much"...
A vent connector is a 'horizontal / pitched' vent pipe section that attaches to a vertical chimney, flue, or vent.
The following is a quote from the AmeriVent installation instructions
General Installation Guidelines
7. Wherever possible, install vertical vents directly above appliances before beginning any lateral runs. Lateral venting should be kept to a minimum to avoid vent resistance. Horizontal runs to vents should be either in accordance with the appropriate tables in NFPA 54, or should not exceed 75% of the vertical height of the vent.
This next quote is from the International Fuel Gas Code (almost the same) (http://publicecodes.cyberregs.com/icod/ifgc/2009/icod_ifgc_2009_5_sec003_par092.htm?bu=IC-P-2009-000007&bu2=IC-P-2009-000019)
503.10.9 Length of vent connector.
A vent connector shall be as short as practical and the appliance located as close as practical to the chimney or vent. The maximum horizontal length of a single-wall connector shall be 75 percent of the height of the chimney or vent except for engineered systems. The maximum horizontal length of a Type B double-wall connector shall be 100 percent of the height of the chimney or vent except for engineered systems.
If none of the above helps, let me know but provide as much information as possible about your installation.