Hi Tyron,
Maybe I can help, you can by all means book all cheap hotel once you are in these countries and yes you will save money if you book it all yourself (versus prebooking with an agency). You will find a great offer of hostels ranging from $3 to $15 per night; although if you want hot water, which is not easy to find in Bolivia and the Andes, you are looking at at least $10 per night per person. A true 3star hotel will range between $30 and $50/night/person.
Regarding the Inka Trail, I highly reccomend pre-booking them well in advance (at least 3 months in advance). It is highly popular and there are limited spaces. I have lived in Cuzco most of last year and you wouldnt believe the hundreds of travelers who arrive to Cuzco to do the Inka Trail only to find out that it is completly sold out. You also have to watch out as in Cuzco many local agencies will sell you anything; for example sell you a different trek but still call it the Inka Trail. There is a lot of that with local agencies. what I do know is that the Inka Trail is fully booked until late October.
I reccomened the following link for more information for the Inka Trail:
http://www.peruforless.com/adventure/adven_incatrail
These guys have great testimonials and the cheapest price guaranteed. They can also help with other parts of your trip.
Ric