Rasulullah sallallahu alayhi wasallam used to go to the toilet with his shoes and also the head covered.(Zaad-ul-Ma'aad)

Read this du'aa before entering the toilet:

Bismillaah, Allaahumma innee a'oozu bika minal khubuthi wal khabaa'ith
O Allah! I seek refuge in You from the foul male and female devils (Shayaateen). (Mishkaat)
Note: Due to the barakah of this du'aa, a veil is created between the rector and the (khabeeth) Shayaateen of the toilet which prevents them from looking at the private parts. It is correct to read both dhammah and jazm on the letter baa of the word khubuth. (Mirqaat Vol., 1 Page 361)
When entering the toilet, first place the left foot. (Now), place the right foot on the foot pad (first and then the left); and when coming off, remove the left foot first. (Zaad-ul-Ma’aad)
When uncovering the body, the more one can lower his body the better. (Tirmizi, Aboo Daawood)
When coming out of the toilet, step out with the right foot and recite (outside):

Ghufraanaka... Al'hamdu lillaahillazi azhaba annil azaa wa 'aafaani
O Allah! I seek Your Forgiveness... All Praise is due to Allah who has removed my harm and has given me sound health. (Mishkaat)
Ring or any other item with visible inscription of a verse from the Qur'aan or the blessed name of Rasoolullaah sallallahu alayhi wasallam should be taken off and left outside the toilet. After coming out of the toilet, it can be worn again. (Nasa'ee)
Whilst relieving, one should neither face the Qiblah nor have his back towards it. (Tirmizi)
Whilst relieving, do not talk without dire necessity. Similarly, do not engage in the remembrance of Allah verbally. (Mishkaat)
Whilst urinating or during istinjaa, do not touch the private parts with the right hand. Use the left hand. (Bukhaari, Muslim)
Safeguard yourself from the drops / splash / sprinkling of urine because generally the punishment in the grave is brought about due to not remaining safe from the drops of urine. (Tirmizi)
Where toilet facility is not available, one should relieve himself in a place where he is out of people's sight. (Aboo Daawood)
Locate soft ground for urinating so that the urine does not splash and the ground absorbs it. (Tirmizi)
Urinate sitting down. Do not urinate standing. (Tirmizi)

Sahih Al-Bukhari Hadith 1.146 Narrated by Abu Aiyub Al Ansari
Allah`s Messenger (saws) said, "If anyone of you goes to answer the call of nature
he should neither face nor turn his back towards the Qibla (when relieving

Anas reported that when the Messenger of Allah (saws) entered the privy to relieve
himself, he (saws) would say, "In the name of Allah. O Allah! I seek refuge in You
from male and female noxious beings (the Shayateen)."
This is related by Bukhari, Muslim, Abu Dawood, Tirmidhi.

Al-Tirmidhi Hadith 359 Narrated by Aisha
When Allah`s Messenger (saws) came out from the privy, he said: ‘(I seek)
forgiveness from Thee, O Allah.’

Al-Tirmidhi Hadith 374 Narrated by Anas ibn Malik