I am not wanting to finish the main story so quick so how can I tell?

The fallout wiki lists the main quests. You could just look at the titles and cross reference where you're at

When things involving finding you son and things related to it are main quest.

Or just keep track of what new quest you get the instant you finish the previous main quest. (At least, so far. Only slightly confusing bit was when Shadows Of Steel triggered during that one MQ section...)

...hmm, does the main quest always sit at the top of the quest list? Something to look at next time I play.

there is no in game distinguishable way to tell. You just have to remember. Try looking up a list of the main story quests online and find it that way.

"...hmm, does the main quest always sit at the top of the quest list? Something to look at next time I play."

No it doesn't, The game doesn't separate the main from the side quests in the PIP boy. The only way to know is to keep track of it yourself or as Thungrim suggests check the wiki.

not very many are that strait forward.

Oh, well. It was a thought.

Or just do a quicksave and start a conversation with the target NPC. If your dialogue responses are

"Concerned father\mother and loving husband\wife"

"Sarcastically concerned father\mother and loving husband\wife"

"I need more information before I give you my concerned father\mother and loving husband\wife response"

"I'll come back later and give you my concerned father\mother and loving husband\wife response"

Then you are looking at the main questline.

nope, the latest quest you recieve goes to the top. So the list of quests effectively lets you know what ones are the oldest. When i get on and am not really sure what i want to do, i start on some older quests that i have been sitting on