good question you can decide the vowel "a" in ( verbs ) by making it in the present tense ex1: سقا or سقى ? " means watered the plants" . If you make it in the present tense it will be يسقي so the " ى " is the correct answer ex2: رنا or رنى ? " means became closer" . If you make it in the present tense it will be يرنو so the " ا " is the correct answer in ( nouns ) you can check it making the name in " muthanna " which means you make two of it ex : عصا or عصى ? "means stick" . if you want to say 2 عصى it will be " عصوان " so the "ى " is not correct and it should be "عصا " you can say the origin of " ا " is " و " and the oirigin of "ى " is "ي " about the "ء" letter there are rules in dictation if this letter came in the end of the word you must look at the vowel of the letter behind it if it was "fatha " you must write it on "ا " if it was "damma " you must write it on "و " if it was "kasra" you must write it on "ى" if it was "sokon" you must write it on the line. if you want to learn more about the "ء " in the middle of the wrod let me know I'll make it easier to you

there is a slight difference but its not important most people don't even pay attention to it ى has a shorter "ah" sound than ا here's a website that explain how to put the "ء" http://www.islamguiden.com/arabi/m_a_r_61.htm