whenever i rope my drum or even re tighten my drum i always soak my head in warm water for 20ish minutes (if you're just tightening the rope then i take hot water and i pour it on top of the skin and rub it in every 3-4 minutes to keep it moist and warm throughout for at least 10-15 minutes. When you wet the skin it allows you to stretch the skin properly and achieve the deep sound you're looking for from your drum. If you try tightening a dry skin... the skin side will sound high pitched (just like the problem you had). When and if you have this problem you can also fix it by wetting it again with warm water (while the rings or whatever is the least tense possible) and then waiting for it to dry up a little bit. Makes ure while its wet with water you rub the skin with a decent amount of pressure so that the skin loosens up and stretches. If it still doesn't work then take moisturizing lotion and/or mustard oil and rub that stuff in. because the oil and lotion is heavier than the water, it helps get the pitch you're looking for quicker than regular water does.
When you cross rope you start at the first hole just like any other roping method and you go down and you skip the nut/bolt that you would usually go to and go to the next one. Do the same with the holes on the skin. Go through one hole on the skin, go through nut/bolt, go through skin and then nut/bolt again and it should look like you're skipping one each time. When you keep going that way you will eventually end up overlapping and thats how you cross rope it.
As far as smacking the skin goes... A dhaga skin, if used properly and not abused and kept and stored properly, lasts a really long time. Having that said, you smacking the skin may or may not take away some life from it but the results you see from applying that sort of pressure to the center of the skin to tune the drum lower do not compare to just smacking the skin with the stick. When you try getting the skin to be a certain pitch that you want it to be, the dhaga only helps so much, the smack actually stretches the skin a little at a time, which in the end gives a lower pitch than a normal dhaga strike would.
Last thing i promise. if you have tiny rips, make sure you put a small piece of tape on the area so it doesn't rip more (don't cheap out and buy tape from the dollar day.... get proper gorilla tape or really good quality duct tape to cover it up or it won't work right)