Br. J.B. Darcy points out some necessary background information: “For centuries, Spain had been almost completely overridden by the Moors. The Spaniards had been trying to take back their country from the Moors for almost 800 years. By the middle of the 15th century, this reconquest was almost complete, but Spain was still a hodgepodge of competing principalities and, because of its constant state of warfare, still a very backward country.” 
As mentioned earlier, Alexander enjoyed good relations with the reigning Spanish monarchs, even as a cardinal. King Ferdinand, while wily and of the arrogant, anti-Roman Aragonese, would often have no choice but to assent to the devout Queen Isabella’s wishes, for “love held their wills in unison”.  Alexander understood this and worked around it.
While papal legate to the country (1472-1473), he exhorted to the clergy, “..I beg of you not only to be of one mind in guarding and defending [the Church] as the most precious thing, but also to spare yourselves neither pain nor peril for its preservation.”  He was also able to convince the people to rise up against the Muslims (which they definitely did, in Granada) and support a Crusade. 
Alexander was, very obviously, a lover of Spanish culture. While legate, he “seems to have had a pleasurable time in his native land, for he stayed there more than a year and many letters from the Cardinal of Pavia were needed to entice him back to Rome.”  Cesare had a great fondness for the culture, as well, including bullfighting. 
One thing that the government would not tolerate from Alexander was his shielding of our rabbinical brethren, the Hebrews, at this time. To their great consternation, the pope made living arrangements for them in Rome, after their expulsion. This, it seemed to them, only undermined the Spanish position. Alexander allowed Spain to tax churches in its territory in response to Spain’s complaints about expenses incurred from its incentivized conversions of infidels. However, he refused to back down when it came to treating people of other faiths with Christian charity.  He tolerated the Spanish Inquisition, but, like Sixtus IV, he tried to rein it in: he personally curbed Torquemada’s power and hired four “assistants” to supervise him. 
The Spanish also were not happy about Alexander’s close relations with the French. But in 1503, “a change [occurred] in the Borgia politics, an inclination to draw nearer to Spain and retire from France consequent on the latter s humiliation”.  It is too bad that death prevented him from capitalizing on this.
There were plenty of healthy developments.
In May 1493, two months after explorers returned from the New World they had just discovered, Alexander published a papal bull marking the boundaries of the territories of Spain and Portugal, entrusting the Americas (minus Brazil) to the former. He wrote, “In these unknown lands where Christopher Columbus has stepped, lives a people, naked, vegetarian, who believe in one God and ask but to be taught to believe in Jesus Christ.” 
The impact of all of this is profound: nearly 50% of Catholics today live in the Americas. In recognition of this, renditions of Native Americans were painted in the Borgia Apartments. “In addition, he installed the golden ceiling of Santa Maria Maggiore, using the precious metal brought back by Columbus and donated to the [P]apacy by Ferdinand and Isabel[la].” 
Alexander also helped reform parishes and convents in Spanish territories, commanded the Spanish bishops to crack down on the forgery of indulgences,  assisted with evangelizing Granada, and extended the indulgence for those still fighting the Moors.  And the monarchs helped him in the “Holy League”, granting him use of their Gran Capitan, Gonzalo Fernández de Córdoba, and more.
2. Warren H. Carroll, Isabel of Spain, The Catholic Queen (http://www.queenisabel.org/AboutIsabel/IsabelOfSpain.html)
3. de la Bedoyere, p. 66
4. Cloulas, p. 45
5. Mathew, p. 50
6. Burchard, p. 131
7. Cloulas, p. 79-80
8. Rafael Sabatini, Torquemada and the Spanish Inquisition (Stanley Paul & Co., 1913), p. 383-384
9. von Pastor, Vol. 6, p. 129
10. Cloulas, p. 78-79
11. Charles A. Coulombe, Vicars of Christ (ISBN 0-8065-2370-0), p. 330
12. Rafael Sabatini, The Life of Cesare Borgia (Stanley Paul & Co., 3rd Edition), p. 165
13. Sabatini, The Life of Cesare Borgia, p. 129