Best way to book travel to Bolivia from Europe/Uk?

Using skyscanner and google flights, both recommend using dodgy looking third party sites to handle the booking that I’m not too happy to book, what are peoples experiences with these sites if they have booked using them? Also, if you’ve avoided them do you just book directly with the airliner and book multiple tickets? Ie, from London to Madrid and then use BoA to book Madrid to Santa Cruz, for example. Is this the standard way for most people where they just manage/handle multiple different tickets? What would happen if say my flight was delayed also and cause me to miss another? Forgive my questions, I’m a rookie at long haul travel and have only been within Europe.