Good questions. Sounds like you might have lost your wheel alignment along the way but that don't matter - most important thing is to get the wheels both in line and this is a good time to do it. The ideal is to get the two wheels properly in line but no need to get too carried away and buy special tools.
Buy a chain alignment tool tool if you like but you don't need one.
For street riding, near enough is good enough. If your wheels are badly out of line, the bike won't drive straight, handling will suffer and your tyres will wear quicker. But you can get them so close, you or I or the average Joe ain't gonna notice the difference.
To answer your question, should you go by the marks or count turns of the adjuster? Counting turns only works for wheels that are already in line, so forget that. Get the rear wheel with the adjusters both at the same hash mark - that puts you in the right ballpark. Then use one of the methods to check the rear is in line with the front. With the bike on the centre stand.
You can use a long straight plank (not all planks are straight) placed maybe on two bricks or mugs, touching the edges of the rear tyre in two places - it will run just wide of the front tyre but the gap should be the same at both leading and trailing edges of the front tyre. Check by setting up the same arrangement t'other side of the tyres and the gaps should be similar. I'm calling the widest part of the tyre the edge.
You can use a long metal angle piece or similar to do the same job.
Or you can do as I do - get down real low ahead of the bike and peer past the front tyre towards the back tyre. Start at the front, because most times the front wheel will be turned a little and you need to nudge the handlebar to put it straight. Because the rear tyre is wider, you shouldn't be able to see the side of it till you move your head a little ways out to the side. As soon as you can see the front and rear sides of the rear tyre, pay attention to how much of the front tyre you can see. Now move you head a little ways out to the other side, till you can see the two edges of the rear tyre. Can you see the same amount of the front tyre as before? If the answer is Yes
, your wheels are in line, job done.
The explanation is very long-winded so a picture of what I mean? When the two edges of the rear tyre just come into view, the angle between the edges at the front will be wider, because the tyre is narrower. Look along the other side and it should be similar.
However, if the edges of the rear tyre come into view before you can see the edges of the front tyre
it means your rear tyre, seen in plan on the right, is squint as shown and you need to correct by using the adjusters.
I also look along from the rear and check the same thing, that the edges of the rear tyre look the same both sides as the front comes into view.
This will make sense as you do it. And when you move the adjusters - might have to kick the rear tyre to make sure it goes snug forward after you loosen an adjuster - you will see the difference they make.
Once you are happy, it all looks symmetrical, the wheels are in line. In future you can use the counting turns method when you adjust the chain. Obviously, you need to check the chain adjustment is still correct after you do the above. Good luck, any questions ask.
PS Skull and I crossed in the post.