You need to add the fibonacci numbers to a list first so you can use them later when you do the division check. Second, you need to take the total out of the loop, because as kgiannakakis said, it will always be replaced by 0. So it should look like this:
endNum = int(raw_input("Enter the end number here "))
divisable_by = int(raw_input("Sum all numbers in the sequence that divide by: "))
# below is the same as "a, b = 0, 1"
a = 0
b = 1
""" gave single letter variables to those above to use in formula below
(longer strings do not seem to work)"""
c = endNum
d = divisable_by
fib_list = []
# while b is less than or equal to the ending number, it will loop.
while b <= c:
print b
fib_list.append(b)
# below is the same as "a, b = b, a+b"
a_old = a
a = b
b = a_old + b
# the below helps with summing the numbers that are divisable by number chosen.
total = 0
for i in fib_list:
if i%d == 0:
total += i
#prints text and number calculated above.
print "Sum of all natural numbers that divide by the number you chose"
print "and are less than the other number you chose is: ", total
This code will also consider the number that you provided as being last e.g if it's 21 and 3 the total will be 24 (21 and 3 dividable by 3) as you wanted. However this is not what your print says 'and are less than the other number you chose is'...so you should consider changing it to 'less or equal'