It sounds like there are two major parts of your application that you need to work on (1) synchronizing your counter operations and (2) synchronizing your analog input (AI).
Since you need to perform four frequency measurements, the easiest way to get the counters synchronized is to supply a common gate and trigger to all four counters so that they start together and all acquire their frequency measurements off of the same input clock/pulse-train. I have attached an application note that discusses a lot of the factors that you need to consider and how to perform multicounter synchronization. Also the following link also gives some more information on triggering multiple counters with a single pulse:
http://digital.ni.com/public.nsf/websearch/CE99A0B2A
9048A2A86256C630062F550?OpenDocument
Along with this, you mentioned wanting to synchronize your analog acquisition with one of the frequencies. I am assuming that this means you want to trigger your analog acquisition based on one of your four frequency signals. I am not completely clear on what your application needs to do here so I would look at what you have and at some of the information online and the shipping examples to see if you can find a good example to show you what you need to do in this case. If you need to set up a retriggerable AI, then remember that your hardware is not retriggerable; however, you can emulate this in software, which can be slow since it is not that efficient and is very system dependent, or you can use two counters to create a continuous pulse train.
Regards,
Michael
Application Engineer
National Instruments