Here's how I make my double-sided PCBs (using presensitized). I hope it helps.
Before printing your design, create 'registers' on them Just like in professional printing, these registers serve as a way to align pages. For me, I use the corners and the perimeter of the board design as my registers. Create a copper track (usually ground plane) on the sides and corners.
1. Have both your top and bottom design laser printed on clean sheet of bond paper. I strongly suggest that you get to print them on separate sheets. It lessens the probability of having the design distorted. Also, Try printing it on any far-end of the paper. I'll explain later why.
2. Find a photocopying machine that uses powder to imprint the copy. Powder photocopiers produce cleaner results. Also, make sure it can also print on acetate. Using the photocopying machine, transfer your design on acetate. Make two copies of each side. Though, you may opt to have a piece if the copy is satisfactory. (I always prefer to have two copies)
Note:
a. You can directly print your designs on acetate. Just make sure they are exact.
b. By experience, when printing or photocopying on acetate, copies tend to come out distorted. The designs tend to shrink or stretch (heat?), thus, I asked you to make a paper printout.
c. As much as possible, try to orient your copy in a way that the side where it is placed will come out of the photocopying machine first. Most distortions happen at the end of the photocopying process.3. Place each copy of the acetate on top of the paper copy. Check to see of the acetate matches exactly the paper copy. If not, redo Step 2. It's very important that every corner and hole match.
If you created a single copy of each side, you may skip this step.
4. Trim the excess acetate from your copies. Just make sure that the first acetate copy of a side has a bigger clearing from the printout compared to the second acetate copy. Do the same on the opposite side. Ex. acetate_copy_top_1 has a clearing of 1.5 inches while acetate_copy_top_2 has a clearing of 1 inch. Tape them together. again, make sure that every corner and hole is aligned.
5. Now, place both top and bottom acetate copies against each other, as if they're both on an actual PCB board.
6. Tape two of its corners (upper-right with lower-left OR upper-left with lower-right). Again, check for misalignment.
You are now ready to expose your double-sided PCB!
Using a UV Box:
1. Peel the protective covering on both sides of the PCB.
2. Insert the PCB at the center of your acetate designs like a sandwich. Align!
Note:
d. Remember the registers I told you about earlier, this is where it comes in handy. With the help of those markings, I know where to center the PCB... right smack at the middle!3. Secure the two corners of the PCB on the acetate (tape at the corners where the acetate's corners aren't taped) with a tape. This will ensure that the PCB doesn't move during the entire exposure process.
4. Expose one side. When done, slowly flip the board then expose the other side.
5. Remove the PCB from the acetate sandwich.
6. Develop.
7. Etch.
Note:
e. When developing and etching, don't let any side touch the developing or etching basin. It'll ruin the design.
f. I suggest you hold it with your fingers... with rubber gloves of course! 
8. Try drilling a whole on one of the through-holes. If comes out on the other side in place, then, CONGRATULATIONS! You've done a great job! If not, practice makes perfect. I've been doing this process several times already. It hasn't failed me yet.
If you're not using a UV Box, make sure you cover the other side that's not being exposed with an opaque object. Use two pieces of glass to sandwich them together.
I hope this helps.
Any comments or suggestions? They are welcomed!
