Those answers don't seem to get to the point. I am literally changing my timing belt so I will tell you the process as you are requesting it. Note, this assumes you removed your timing belt and have lost your original position of the cam and crank.
The cam is the gear on the top of your engine.
The crank is the gear behind the passenger tire.
The giant black pulley cover thing you see that has the serpentine belt on it is your harmonic balance.
This uses a 6mm alan for the 4 round bolts but careful they strip easy.
If its strips use a propane torch and take a strong hammer and pound a torx bit (slighter larger than the hole) into the alan hole and unscrew it after you torched the hell out of the bolt. It will be hot so watch out. You can measure the bolt and find a replacement pretty easily.
Take off your harmonic balance and you will see the crankshaft gear. The picture above shows marking on the crank that you won't have and definitely don't align your gears off of someone's pictures that's ridiculous.
The cam pulley on the top of the engine will have a mark on the pulley its self and on the engine. Mark these with some white paint or use a paint marker from Walmart so its easier to see. Once you have these lined up attach your pulley holder (rent this from oreilys ask for a cam holder) mine was 130$ to rent and I get that back when I return it.
That will have little clamps that will hold your pulley in place. You will need it to remove the pulley and replace the seals if you're doing that. I am so I included that step.
Now the window your mentioning is pretty much in the same general area on all VW's from 01-now. It's on your bell housing. Its not easy to find because most of the people on you tube have poor camera skills. I hope to fix this in the future with more time by doing a video of a start to finish.
Window location: Find your coil pack. It will be to the left of the power steering (i have a 04 VW new beetle with the Mexican 2.0 "BEV") under your coil pack to the right of it once you remove it (mark your spark plugs and your coil connection spots so you can re-attach them easy). You may have a negative battery ground cable that needs to be removed. It's a 10 mm. The coil uses a 5mm I believe or a 6, I can't remember.
Then you will see the window and the circle hole that may or may not have a plug covering it. Mind didnt. Ignore that hole. Spin your crank until you see this circle with a line through it kinda like this -0- it will be etched in the metal. This is one of your TDC's. Yes there are two. Your crank has a 180-degree offset because of the compression and exhaust stroke.
To find whether your on point or off by 180 degrees. Put your finger or something in the piston one location. Furthest left for most but google your engine to make sure.
When you fee the gust of air or pressure your on the compression stroke. Now make sure that symbol is rotated to the bottom of the window (or more accurately the edge of the window closest to the bumper and NOT the firewall.) The symbol is not TDC in the middle of the window it needs to be at the point where it's about to disappear from sight.
Now make sure your cam is still at its position as mentioned before. Now you are timed. You will need to attach your belt and make sure you hook up all your connectors. It's easy to miss a cable or wire and think your car is not running but you forgot to connect something.
Also, do a spin test on your crank with he belt on to make sure your marks return when rotated. Do not use the belt as a marking point. The belt will never re-align because it's not designed to. It takes upwards of 50 rotations for your belt to hit the same tooth so just forget about the belt being aligned because it doesn't matter. All the markings will be made on metal, not on the rubber belt.
Changing the seals, the pump is its own task but if you can get your car timed you should be able to do these tasks with some ease. And yes you have to remove your passenger engine mount to get the belt out. If you don't know the difference between your serpentine belt and the timing belt then don't change this yourself as you do not have the experience to prevent your piston from smashing your valves. If its a dual overhead cam (two pulleys) like on dodge neons then just make sure both cams are aligned.
Also, keep in mind there are two sensors. A cam and crank sensor. Two different codes are thrown on your OBD. Make sure you match the codes because a crank sensor is easy to change and it's next to the oil filter base. One 5mm alan takes it's off.
The cam sensor sucks and yes your right you have to bet into the pulley and thus you should change your pump and belt while your in there so you don't have to do this job again for a while.
Both sensors are cheap but change your crank sensor first and see if it fixes your issues.
DO NOT DO NOT DO NOT DO NOT attempt to run your engine if the timing is off. You will bend your valves and possibly damage your rocker arms and will have to remove your heads and do a valve replacement and that's fun not fun job.
The goof that worked on the beetle I bought before I had purchased it tried to do the work himself and lost the timing. Normally I wouldn't mess with the gears and make sure they stay in place during a change out but that's a perfect world. You need to learn how to fix issues when you at the starting point and not when everything is perfect. you'll become a better mechanic that way.
Hope this helps.