Hi from Quito
I think if you have only 8 days you do need to decide if you just visit Galapagos or just visit the mainland of Ecuador - I don't think it is enough time to do both. There are 4 day / 3 night cruises available, but it is expensive to get there - flights from mainland over $500 each, then the entrance fees etc. it does seem a waste if you only have the 4 days there (taking into account that 2 of those days will be travelling and you will only get 2 full days on the islands).
In 8 days you can undertake a good tour of the Andes - for example an Avenue of the Volcanoes tour which takes you down the centre of the Andes from Quito to Cuenca. Or do an Eastern Andes & Amazon loop which as well as the Andes takes you down into the Amazon.
With 8 days you should be able to get to see quite a bit travelling independently but you would need to keep a tight schedule and be realistic about what you can achieve!
If you go for an organised tour I imagine you would end up seeing a bit more/covering more ground since things would be organised for you.
Both options have pros and cons - cost, flexibility, freedom, etc. so it depends what is more important to you.