Yes, if your application is installed in /home/picloud, your function will be able to access it by either using the absolute path ('/home/picloud/yourprogram'), or, preferably, by its relative path ('yourprogram').
You can change your working directly after invoking cloud.call(), by including in your function:
def your_function():
if cloud.running_on_cloud():
import os
os.chdir('new_dir')
# the rest of what your function does
Using cloud.running_on_cloud(), we can ensure that the working directory is only changed when your function is being run on PiCloud. Also, you can see how you could install your software to somewhere like '/usr/local/yourprogram', and simply chdir into it when necessary.
Ken