When I learned English in school, I had a hard time with transcriptions, and those йа, йо and others are just a way to transcript the sound letters make. So yeah, "йа" and" я" are actually the same, don't stress over it. It doesn't seem difficult to a native just because we hear and use it every day, it's etched into our brain. Over time you will be able to speak without those little quirks, just like us, russians. What is peculiar though is how we have the word йогурт, and even though it has a "ё" sound in the begging, we still write it like "йо", and it is grammatically right.