I’m not an expert in Beds lace, but I’ve done a bit. I would suggest using ordinary pins (but not those with glass heads, obviously). I use the same pins for the picots. And as for leaving them sticking up or pushing them in – leave them sticking up until they get in the way, then push them in! Much as for Torchon (if you were doing a Torchon mat, for example). there’s a bit more twisting and turning for Beds, but it’s fairly obvious if a pin is getting in the way!
You may find my website helpful. I must repeat – I’m not an expert on Beds, but I’ve done a little, and my website shows you how to do things like picots.