I recently signed up for FF miles and emailed the airline to add my future trip to the FF account.

Names are:
John Smith
John Smith Jr

Smith Jr is the last name (I filled out the FF account according to how my son's passport is, with Jr being in the Family/Last Name)

They were unable to add the flight to my son's account because they said the name was a mismatch.

Up until this time, I was using the website the travel agency sent me to which showed my ticket information, of which, had my son's name listed correctly (John Smith Jr).

But I checked the actual airlines (both airlines) and it shows the name:
Johnjr Smith

While, I don't care about the FF miles as much, I am wondering if it will affect the actual flight and checkin.

I'm a bit confused by this post, since some of it reads as if it's about you ("my future trip") and some as if it's about your son ("unable to add the flight to my son's account"). I assume you know that you are not supposed to earn miles for your son's flights and vice versa, though some sr./jr. pairs have reportedly gotten away with pooling their miles in this way (as long as they're not both in the air at the same time on the same airline). Perhaps you could clarify who's who and who's doing what here?

If this is about your son, then based on a lot of personal experience with a badly screwed up name:

1. It may affect the check-in agent's ability to find his reservation by name, and hence to issue a boarding pass. Have his reservation code (usually six characters) available as an alternative way to access it.

2. It may affect automatic frequent flyer credit, since he may fail the computer's name-number match. Follow the airline's missing credit process if that happens.

It will not affect his clearing security, in flying once he has been issued a boarding pass, or in any other way.

i am mainly concerned about my son getting his boarding pass and clearing security, and not being stopped because of the name issue. I read that the names have to match exactly (first and last name), and that they check it at security (?) which is why I am worried.

I signed up seperate FF accounts for my flight and my son's flight. during that process of adding the flight to each respective account, is when I found out the name was different (showing as "Johnjr Smith", rather than "John Smith Jr"). As far as the FF credit, not worried about it as much as I am clearing security

John Smith <--me
John Smith Jr <-- 7 year old son

we both fly out June 16. I have all the reservation codes, so I will be sure to bring that.

It just looks like the first name is Johnjr rather than John, so was thinking maybe it might be an issue when trying to board/clear security/checkin/etc

It will not be an issue at all, don't worry about it.

Onto a totally different subject - You mention passport, so I'm assuming it's an international flight, if that's the case and it's just you and him traveling, make sure you have a statement from the mother saying it's OK if she's not flying with you. Totally possible you will not be asked for it, but some countries may ask for it.

Yeah, it is an international flight. Would I just need a statement signed by her?

My mother will also be flying, but will be coming back at a later time. I fly back mid-July, and was leaving my kids with my mother and family, of which they fly back mid-August. will I need something for that also, since they will be flying back with their grandmother (without me) ?

edit: did some searching, looks like I will get 2 notarized letters just in case. or, just have 1 notarized letter allowing the grandmother to travel with the kids. (technically, my kids are on the same flight booking with my granddmother, since they are traveling on the same date, while my ticket is on seperate booking).