Not everything the pope says has equal weight. For example, something in an interview, such as the recent controversial one over civil unions, has no weight whatsoever. Some statements we are called to respect but we don't have to internally assent to; others we must believe with the full weight of faith. Canon law, which governs the Church, has this to say:
Canon 749 §1.† By virtue of his office, the Supreme Pontiff possesses infallibility in teaching when as the supreme pastor and teacher of all the Christian faithful, who strengthens his brothers and sisters in the faith, he proclaims by definitive act that a doctrine of faith or morals is to be held.
§2.† The college of bishops also possesses infallibility in teaching when the bishops gathered together in an ecumenical council exercise the magisterium as teachers and judges of faith and morals who declare for the universal Church that a doctrine of faith or morals is to be held definitively; or when dispersed throughout the world but preserving the bond of communion among themselves and with the successor of Peter and teaching authentically together with the Roman Pontiff matters of faith or morals, they agree that a particular proposition is to be held definitively.
§3.† No doctrine is understood as defined infallibly unless this is manifestly evident.
Canon. 750 §1.† A person must believe with divine and Catholic faith all those things contained in the word of God, written or handed on, that is, in the one deposit of faith entrusted to the Church, and at the same time proposed as divinely revealed either by the solemn magisterium of the Church or by its ordinary and universal magisterium which is manifested by the common adherence of the Christian faithful under the leadership of the sacred magisterium; therefore all are bound to avoid any doctrines whatsoever contrary to them.
§2.† Each and every thing which is proposed definitively by the magisterium of the Church concerning the doctrine of faith and morals, that is, each and every thing which is required to safeguard reverently and to expound faithfully the same deposit of faith, is also to be firmly embraced and retained; therefore, one who rejects those propositions which are to be held definitively is opposed to the doctrine of the Catholic Church.
Canon 752 † Although not an assent of faith, a religious submission of the intellect and will must be given to a doctrine which the Supreme Pontiff or the college of bishops declares concerning faith or morals when they exercise the authentic magisterium, even if they do not intend to proclaim it by definitive act; therefore, the Christian faithful are to take care to avoid those things which do not agree with it.
Code of Canon Law as stated on the Vatican website.
Thus Catholics are expected to at least a religious submission of the intellect and will to what the teaching office (Magisterium) of the Church says, and in other cases a teaching is infallible (i.e. certain by faith) and we must firmly embrace what She teaches.
One thing that must be kept in mind when contemplating reception into full communion with the Catholic Church is that it is not a correct motivation to become Catholic because one believes She teaches the truth. Rather, one must trust the Church as a truth-telling thing/organization.
It is the Church that is the standard by which we measure what we believe; it is not our belief by which we measure the Church. When you become Catholic, you accept what She teaches now, and forever into the future. You look to Her to instruct you, not to affirm your opinions.
So to answer your question:
- What should I do if I disagree with the pope on any issue?
If the pope has ruled definitively on a matter of faith and morals (which happens relatively rarely), one must believe with divine and Catholic faith what he has defined. To refuse to do so would constitute heresy. If the pope has taught authoritatively on a matter of faith and morals but not definitively, one owes a religious submission of the intellect and will to that teaching.
There are many elements of what the pope says that are not considered teachings (for example, disciplines, or the infamous interview). For these elements one may prudentially and respectfully disagree with the pope.
If you want a book that helps:
- sort out which teachings are definitive and which aren't, and
- helps you in understanding the weight of different documents . . .
I recommend Teaching with Authority by Jimmy Akin.