What I do is:
Leave one large chest near the stairway. Store extra weapons, bottles of liquids, and unnecessary scrolls and wands in this chest. Carry it with you to each new level, but leave it right at the stairway. Leave another chest full of spoilable food on the previous level, not on the level you are currently exploring.
Then carry a smaller chest. In this one take your essential scrolls and wands (teleport). Use it as a temporary holding place when you find new bottles or spoilables as you explore. Every now and then go back to your large chest and drop these off. Carry healing liquids in cans not bottles. Carry one wand of teleport outside of the small chest, keep the rest inside the chest.
Now you have everything. Healing liquids in a can, an easily accessible wand of teleport, and useful scrolls and wands protected but accessible. Explosives, fragile objects, and objects that you don't want other monsters picking up are stored in a safe location without burdening you unnecessarily.