should you continue to charge apple watch if you are not using it for a long time (more than 2 weeks)?

According to Apple Watch Battery and Performance:

"...keep Apple Watch half-charged when it’s stored for the long term."

Yes you should,an apple watch battery should never be allowed to go completely dead for any length of time;

Lithium-ion batteries contain a protection circuit that shields the battery against abuse. This important safeguard also turns the battery off and makes it unusable if over-discharged. Slipping into sleep mode can happen when storing a Li-ion pack in a discharged state for any length of time as self-discharge would gradually deplete the remaining charge.All batteries are affected by self-discharge. Self-discharge is not a manufacturing defect but a battery characteristic.

Information from;

batteryuniversity.com