If you can mark the part where it won't show. I have great luck with Sharpy pens, silver and gold, they don't rub off. I agree with others too, soap is great. What I like with the soap is that it shines under the light so it makes it easy to see.

If you are looking for mechanical pencil I would recommend the Sewline
Mechanical fabric pencil (white). You can draw fine lines with it.
I use both black and white. The black one is very useful for marking HST's.

I should have added that the soap marks will disappear immediately if you hold a steam iron over--don't touch or press--just the tiny bit of steam.

I use the Bohin mechanical pencil with white lead on my dark fabrics. I find it stays on well during the quilting process but washes out with no issues. On light fabrics I usually just use a #2 mechanical pencil. But if I think of it next time I'm in a LQS that sells the pencils and leads, I'll get a different color for the light fabric as I'm hoping it will wash out a bit better. As long as I don't get too heavy handed with the #2 lead, it's okay. I have also evolved to marking as I go most of the time vs marking the entire quilt. I personally have not had much luck with the soap slivers or typical 'taylor's chalk'. I have issues with them fitting into the stencils.

Another "AMEN" for the Clover white pen. It totally rocks. Also agree on "wait a sec for the marks to appear." They sort of "fade in." The markings are rock steady but wash or iron out perfectly, especially if you prewash your fabric. The ONLY time I had an issue seeing the marks was on some fabric I had failed to wash, and it had a TON of nasty sizing, which seemed to suck the markings. Sizing irritates my skin too, so I prewash 99% of my quilting fabrics.
I'm a hand quilter too and I ruddy HATE the grittiness of chalk.

I use the purple disappearing pen for light fabrics. In summer if you do not AC, it disappears REALLY quick.

I tend to prefer a chalk wheel for dark fabrics. Finer line than using a chalk stick but till washes out easily.

i use frixion pens for all that i can. I have used the white ceramic pencils pretty successfully for marking dark fabrics.

I use the "silver" marking pencils for dark fabric.

Another vote for white bar soap.

I'm gobsmacked by the thought of marking my quilt top with a silver or gold Sharpie.... :shock::shock::shock:

I use a light box and Crayola Ultra-Clean fine tip markers or a white chalk pencil.