I'd go for something along the lines of Wilkinson1998.
Premier League: (16)
Celtic, Aberdeen, Hearts, Dundee United, Dundee, Hamilton, Ict, Ross County, Partick Thistle, Kilmarnock, Motherwell, St Johnstone, Rangers, Hibs, Falkirk, Raith
Championship (16)
Morton, St Mirren, Queens, Livi, Dumbarton, Alloa, Ayr, Dunfermline, Stenhousemuir, Albion Rovers, Airdrie, Peterhead, Forfar, Stranraer, Brechin
League One (16)
Arbroath, Annan, Montrose, Elgin, Stirling, East Stirlingshire, Berwick, Clyde, Queens Park, East Fife, Auchinleck Talbot, Bo'ness United, Bonnyrigg Rose, Rob Roy, Linlithgow Rose, Pollok
Would go with the top league being the current top 16 in the country, followed by the lower 16 in a championship league, followed by league one with the bottom league with addition of the top 6 junior teams (or biggest supported clubs - just an example of junior teams)
Then join the remaining non league seniors and juniors into a similar concept to create the pyramid of 3 up / 3 down - a Scottish Conference if you will, followed by North / East / West regions below that.
I liked the idea of allowing all teams in Scotland from Amateur to Seniors being allowed to participate (if they wanted) in "big" Scottish Cup and allow smaller clubs to also participate in their Junior / Amateur Scottish Cups.