If you use CM14, for 1 Nation team I suggest to you to simply replace an existent team (North Ireland for example) in Team section. You should change kit,players, flags and, obviously, the id.
In roster use call option, not transfer.
I think also you should change the map section. I'm not 100% sure of this because I've never edit national teams.
To create the League:
I say to you that there are many tutorials or something like this in this forum,so you can search.
I explain to you how I created lower Italian leagues, working in career mode. Again I'm not 100% sure because i edited an ingame country, I think you'll have to create Israeli in Tournament tab (I'll try something like this for UCL qualify when I'll have time).
I think this should work however...(continue)
I'll post pics for example.
1. Create a league and its teams (I think you know,otherwise search in forum), look a similar league to see different things (ALJ e K league have 14 teams), red arrow it's for Europ cups qualifying.
2. In Tournament tab you should create Israeli (not sure for this step)
3. Copy and paste a trophy (for example K league). Copying a trophy you'll have the copying trophy rules: don't know exactly how change them (there are lots and different options), I suggest to you to prove without edit and back up, if you don't like you can try changes after back up.
4. In this new trophy you'll have to change the league to take teams from.
5. Scroll down to put qualifying rules. I suggest to you not to edit calendar, unless you know it well.
6. Euro cups qualifying: this is my edited one,so yours will be different, pay attention to numbers. Simply click and choose numbers and rules (the top number is the total for each section. G1 is the winner, G2 are teams direct to groups, G3 are teams to play-off. Same for UCL and Euro League.