She seemed thoroughly at ease on horseback.

Literal

She [topic-は] horse-back [on-で] very is-relaxing [as-ように] looked.

馬上 ('on horseback') is a slightly literary noun. で here marks the location of the relaxing action. ~ように見える ('look like, appear to be') here uses an embedded clause (くつろいでいる) as its object — 'looked like she was relaxing.'