Clock synchronization between Cortex-A9 and Cortex-M3
It seems to me that you're a bit confused about what exactly you're supposed to do and are incorrect connections between things. 

First, did you read up on UTC? Basically, the GPS unit you have should output its time using UTC time zone and, as far as time synchronization is concerned, UTC is no longer of interest. You may want to translate from UTC to your own time-zone, but that's not related to clock synchronization.

Next, your Cortex A9 should receive the time and set its own RTC to the time sent by the GPS. In order to have as correct time as possible, it would be a good idea to use the PPS output of the GPS to trigger the procedure which will set-up the RTC time on the A9. This is where the "precision" comes into play. It takes some time for RTC to be set up and your RTC will be late by that amount of time. Usually, that won't be a problem, since the amount of time is very short, but some attention may be needed in order to be sure that nothing interrupts the time-adjustment process. 

Finally, you have the problem of synchronization between the two microcontrollers. As far as I understand it, you want to transfer time from A9's RTC to the M3's RTC using SPI. SPI clock isn't too important here. A9 will send clock (not the wall clock!) and control the data transfer speed. Again, you'll have similar problem to setting up the RTC on A9. Transfer of data from the A9 to M3 takes some time and M3's clock will be late by that amount of time, unless you try to do something to avoid that (if it's worth doing in the first place). 

So a way to do this is to adjust the A9's RTC so that its second passes as close as possible to the PPS signal of the GPS. Next, right after the PPS signal, initiate transfer from A9 to M3 in order to be as little late as possible. 

How precise you can be also depends on the RTC timer itself. Some may allow you to pause their time count. This way, you can set up the time on RTC in advance and then count down the PPS from GPS until that time comes (for example, when it's 13:26:26, set the time to 13:26:27 and enable the RTC when 13:26:27 is counted by PPS). It will usually be faster to enable RTC than to set up its time. This way, you can be a bit closer to the actual UTC time, but the process will be a bit complicated.