Visited November 2014. Easy if you are in Samaipata town (recommended to stay a bit longer). The easiest way to get to El Fuerte is by foot (some 9 km from Samaipata town). If bad weather or lack of time the most economic way is to take a moto-taxi from just outside the mercado (cost for one way should be 20 B per person - moto-taxi takes only one person at a time), car-taxi for a full trip will want more, there is no other public transport there (well of course there is a possibility to arrange a trip from local agency - costs more ....).
Joint ticket for foreigners (50 B per person, a little bit too much as for Bolivian standards) entitles to visit a site of El Fuerte and a local museum in Samaipata town (two halls, some plans, ceramics).
As mentioned El Fuerte is located 9 km from the centre of Samaipata (direction of Santa Cruz), the road is just being paved (2/3 of the job is now done) so next year they will surely have excellent road there. For the whole site 3-4 hours should be enough to see - take some water with you.