Good manners of Jihad:

Allah says:

]يَا أَيُّهَا الَّذِينَ آمَنُواْ إِذَا لَقِيتُمُ الَّذِينَ كَفَرُواْ زَحْفاً فَلاَ تُوَلُّوهُمُ الأَدْبَارَ. وَمَن يُوَلِّهِمْ يَوْمَئِذٍ دُبُرَهُ إِلاَّ مُتَحَرِّفاً لِّقِتَالٍ أَوْ مُتَحَيِّزاً إِلَى فِئَةٍ فَقَدْ بَاء بِغَضَبٍ مِّنَ اللّهِ وَمَأْوَاهُ جَهَنَّمُ وَبِئْسَ الْمَصِيرُ[
(الأنفال: 15 - 16)

This means: “O you who believe! When you meet those who disbelieve, in a battle-field, never turn your backs to them. And whoever turns his back to them on such a day - unless it be a stratagem of war, or to retreat to a troop (of his own), - he indeed has drawn upon himself wrath from Allah. And his abode is Hell, and worst indeed is that destination!”
(8, Al-Anfal: 15 - 16)

The Messenger of Allah (peace be upon him) said:

“When you meet your enemies who are polytheists, invite them to three courses of action. If they respond to any one of these, you also accept it and withhold yourself from doing them any harm. Invite them to (accept) Islam; if they respond to you, accept it from them and desist from fighting against them. If they refuse to accept Islam, demand from them the Jizyah. If they agree to pay, accept it from them and hold off your hands. If they refuse to pay the tax, seek Allah’s help and fight them.”
(Reported by Abu Dawud and Muslim)

The Prophet (peace be upon him) also said:

“Go in Allah’s Name, trusting in Allah, and adhering to the religion of Allah’s Messenger. Do not kill a decrepit old man, or a young infant, or a child, or a woman; do not be dishonest about booty, but collect your spoils, do right and act well, for Allah loves those who do well.”
(Reported by Abu Dawud)

He (peace be upon him) also said:

“Never betray.” (Reported by Muslim)

The Prophet (peace be upon him) said:

“When Allah will gather together, on the Day of Judgment, all the earlier and later generations of mankind, a flag will be raised (to mark off) every person guilty of betrayal, and it will be announced that this is the perfidy of so and so, son of so and so (to attract the attention of people to his guilt).” (Reported by Al-Bukhari and Muslim)

He (peace be upon him) also said:

“If you find so-and-so, kill him, and do not burn him, for no one punishes with fire except the Lord of the fire.”
(Reported by Abu Dawud)

Samurah Ibn Jundub (may Allah be pleased with him) narrated:

“The Prophet of Allah (peace be upon him) used to exhort us to give charity (Sadaqah) and forbid us to mutilate (a slain).”
(Reported by Al-Bukhari)

He (peace be upon him) also said:

“The most merciful of the people with respect to killing are believers (in Allah).” (Reported by Abu Dawud)

  He (peace be upon him) also said:

“Supplications at two times are never turned down or (are seldom turned down): a supplication made while the Adhan is being proclaimed and one during the battle when the fighting is at its utmost.” (Reported by Abu Dawud)

He (peace be upon him) also said:

“O Allah. Revealer of the Book, Disperser of the clouds, Defeater of the hordes, put our enemy to rout and help us against them.”
(Reported by Al-Bukhari and Muslim)

Booties gained without fighting:

Allah says:

]وَاعْلَمُواْ أَنَّمَا غَنِمْتُم مِّن شَيْءٍ فَأَنَّ لِلّهِ خُمُسَهُ وَلِلرَّسُولِ وَلِذِي الْقُرْبَى وَالْيَتَامَى وَالْمَسَاكِينِ وَابْنِ السَّبِيلِ إِن كُنتُمْ آمَنتُمْ بِاللّهِ وَمَا أَنزَلْنَا عَلَى عَبْدِنَا يَوْمَ الْفُرْقَان [ (الأنفال: 41)

This means: “And know that whatever of war-booty that you may gain, verily one-fifth (1/5th) of it is assigned to Allah, and to the Messenger, and to the near relatives [of the Messenger (Muhammad SAW)], (and also) the orphans, Al-Masakin (the poor) and the wayfarer, if you have believed in Allah and in that which We sent down to Our slave (Muhammad SAW) on the Day of criterion (between right and wrong).” (8, Al-Anfal: 41)

Allah says:

]مَّا أَفَاء اللَّهُ عَلَى رَسُولِهِ مِنْ أَهْلِ الْقُرَى فَلِلَّهِ وَلِلرَّسُولِ وَلِذِي الْقُرْبَى وَالْيَتَامَى وَالْمَسَاكِينِ وَابْنِ السَّبِيلِ كَيْ لا يَكُونَ دُولَةً بَيْنَ الأَغْنِيَاء مِنكُمْ[ (الحشر: 7)

This means: “What Allah gave as booty (Fai') to His Messenger (Muhammad SAW) from the people of the townships, - it is for Allah, His Messenger (Muhammad SAW), the kindred (of Messenger Muhammad SAW), the orphans, Al­Masakin (the poor), and the wayfarer, in order that it may not become a fortune used by the rich among you.” (59, Al-Hashr: 7)

Poll taxes (Jizyah):

Allah says:

]قَاتِلُواْ الَّذِينَ لاَ يُؤْمِنُونَ بِاللّهِ وَلاَ بِالْيَوْمِ الآخِرِ وَلاَ يُحَرِّمُونَ مَا حَرَّمَ اللّهُ وَرَسُولُهُ وَلاَ يَدِينُونَ دِينَ الْحَقِّ مِنَ الَّذِينَ أُوتُواْ الْكِتَابَ حَتَّى يُعْطُواْ الْجِزْيَةَ عَن يَدٍ وَهُمْ صَاغِرُون[ (التوبة: 29)

This means: “Fight against those who (1) believe not in Allah, (2) nor in the Last Day, (3) nor forbid that which has been forbidden by Allah and His Messenger (4) and those who acknowledge not the religion of truth (i.e. Islam) among the people of the Scripture (Jews and Christians), until they pay the Jizyah with willing submission, and feel themselves subdued.” (9, At-Tawbah: 29)

Reconciliation:

Allah says:

]كَيْفَ يَكُونُ لِلْمُشْرِكِينَ عَهْدٌ عِندَ اللّهِ وَعِندَ رَسُولِهِ إِلاَّ الَّذِينَ عَاهَدتُّمْ عِندَ الْمَسْجِدِ الْحَرَامِ فَمَا اسْتَقَامُواْ لَكُمْ فَاسْتَقِيمُواْ لَهُمْ إِنَّ اللّهَ يُحِبُّ الْمُتَّقِين[ (التوبة: 7)

This means: “How can there be a covenant with Allah and with His Messenger for the Mushrikun (polytheists, idolaters, pagans, disbelievers in the Oneness of Allah) except those with whom you made a covenant near Al-Masjid-al-Haram (at Makkah)? So long, as they are true to you, stand you true to them. Verily, Allah loves Al-Muttaqun (the pious).” (9, At-Tawbah: 7)

The Prophet (peace be upon him) said:

“We will fulfill the covenant made with them and seek Allah’s help against them.” (Reported by Muslim)

The Prophet (peace be upon him) said:

“If anyone kills a man whom he grants protection prematurely, Allah will forbid him to enter Paradise.” (Reported by Al-Bukhari)

He (peace be upon him) also said:

“I do not break a covenant or imprison messengers.”
(Reported by Abu Dawud)