Ok, if i am reading your questions correctly, limiting the read write to eprom is a good thing, they only have limited read write cycles anyway, so less here is more.
Next, if you are limiting when you write to eprom to only say on bootup and on shutdown, then doing it all in one call is a good thing, this becomes 1 write cycle to eprom
MyFunc(var_1, var_2, var_3);
and this while functionally the same is 3 writes,
MyFunc(var_1);
MyFunc(var_2);
MyFunc(var_3);
Now depending on how long your data string is, you might need to break it up into a couple of calls anyway, if you are hitting the memory limits and the like. Also, if you really need to read and write to file often, you might need to add an sd card to your project and read and write to file rather than eprom.
Hope I followed your questions correctly as was helpful.
rob.