Edinburgh and Glasgow are very different and Glasgow is a lot less touristy than Edinburgh. Both have world class attractions and museums - think the Burrell and Kelvingrove in Glasgow. It is worth spending some time in both.
Glasgow is a good base if you are wanting to use the line to Oban and places north, Loch Lomond or down the coast to Ayr (for Culzean Castle) or across to places like Bute, Arran, etc.
Edinburgh is a good base for St Andrews, Dundee, and the north.
Stirling can easily be done from either Glasgow or Edinburgh.
Inverness is a base for the far north line to Wick and Thurso, the Kyle line to Kyle of Lochash, the line to Elgin and Aberdeen, or back down the line to say Aviemore. Places like Culloden and Clava Cairns are easily done by bus from Inverness. You can catch a bus to Fort William (runs along the side of Loch Ness) which gives access to the West Highland Line.
I assume you have found the website for the
Spirit of Scotland Pass? If not it is worth spending some time on it. There is a useful map and it also gives suggestions for holidays from either Glasgow or Edinburgh.
Plan out what you are wanting to do as you may find that 8 travel days out of 16 aren't enough!!! You may end up having to pay extra for days not covered, depending on what you have planned.
Work out how you intend to get to Skye - either bus from Kyle of Lochalsh or ferry from Mallaig to Armadale. Portree is the main centre and without a car is possibly your best place to stay. Bus services on Skye aren't brilliant - more designed to get people to and from work or kids to and from school than for tourists.
Brae Bikes in Portree does hire e-bikes.