Lot's of good advice, here, especially not smoking the bottom of the bowl if you're not enjoying it. No reason to suffer through something that doesn't bring you pleasure!
I routinely smoke to the bottom. It took me a while to get there, but to me, it was worth the journey. The first thing was learning not to pack the bowl so tightly. It made a huge difference for me, both in the way the tobacco tastes, and the way it smokes. The second was learning not to tamp so much or so hard. The weight of the tamper is usually more than sufficient to "settle" the ash and make re-lighting possible. I used pack the pipe too tightly, and tended then to poke and prod and play with the ash top so much that, despite my good intentions, it became impossible to get the resulting brick of soggy tobacco to light with anything short of an oxy/acetylene torch.
As you travel down this strange road we're all on, your habits will probably change and develop into what works best for you. Some folks love the last 1/4 of the bowl the most, others don't. They're all right, as long as they're enjoying what they're doing. It's no crime to dump the last part of the bowl. I once knew a guy that loved vintage Three Nuns, but only enjoyed the first half of the bowl. He'd buy new TN to fill the bottom, then top it with his treasured vintage stuff and enjoy the hell out of it. Half way through, his smoke was done, and he was happy not to have wasted his precious gold.
As far as "ruining" the pipe goes, it will be necessary to maintain the cake a little more carefully to prevent a very uneven surface. After finishing the bowl, but it's not going to kill the pipe as some might think. It will likely result in a "sour" heel if the pipe is smoked too much without letting it dry, but that's not the end of the world, either. Swab it out, shake the ash, do whatever works for you, and just keep an eye on it. When the ridges start to be noticeable, a little reaming will make things right again. When the taste starts to suffer, a few pipe cleaners and a little alcohol (cheap vodka is great for pipe cleaning) will help. MOST of those "off tastes" result from gunk in the shank, anyway, not gunk in the bowl.
And, whatever you do, enjoy it. Pleasure over panic is what pipe smoking is all about, as so many have said.