Adam Clarke on Psalms 99:5

Worship at his footstool - Probably meaning the ark on which the Divine glory was manifested. Sometimes the earth is called God's footstool, Mat 5:35; Isa 66:1; sometimes Jerusalem; sometimes the temple, Lam 2:1; sometimes the tabernacle, Psa 32:7; and sometimes the ark, 1Chr 28:2. The Israelites, when they worshipped, turned their faces toward the ark, because that was the place where was the symbol of the Divine Presence.

For he is holy - The burden chanted by the chorus.