Are all compounds made of ions?

No. In fact no compounds are made entirely of ions. Every chemical bond, even those with high ionic character all have some covalent character, and so there are no compounds with 100% ionic bonds, hence no compounds entirely composed of ions. The only time you have actual ions are when the compounds have separated as in an aqueous solution.

From the remainder of your question, it looks like you have an issue with nomenclature rather than bonding. Instead of ionic charges, you should be thinking in terms of oxidation numbers. I know, there are too many numbers with pluses and minuses, but it is oxidation number that is what you want. Oxidation numbers are values that are assigned to elements (frequently relating to the number of electrons available bond bonding) to use in figuring out formulas (among other things).

For instance, calcium is in group IIA and therefore has an oxidation number of 2. Phosphate has an oxidation number of -3. When atoms and polyatomic ions combine to form compounds they do so in ratios so that their oxidation numbers will add up to zero.

Ca2+ and PO4^3- combine with three Ca2+ and two PO4^3-. That way the oxidation numbers will add up to zero.

+2 +2 +2 ..-3 ...-3 = 0

Ca Ca Ca PO4 PO4

Here is a tutorial you might find useful:

http://lac.smccme.edu/New%20PDF%20NovaNET/oxnum2.p...

Here is another one: http://chemed.chem.purdue.edu/genchem/topicreview/...

And here is a periodic table with some common oxidation numbers. Pay attention particularly to the ones in red. Notice how the oxidation numbers are related to the columns of the periodic table.

Here are the oxidation numbers of some polyatomic ions. In this case the oxidation number is the ionic charge. http://www2.pvc.maricopa.edu/tutor/chem/chem130/no...

for compounds, yes you always need to know the charge for each and then pretty much "criss cross" the charges and those numbes become the small number (sub-something, forgot the word).

Ca must have a charge of 2 (probably -2, bad memory)

and PO$ must have a charge of 3

the only atoms that don't have a charge (generally) are noble gasses (the last row)

You have to take in account the charges of the cations and the anions while considering the formation of the polyprotic cations or anions.

Sodium Bicarbonate is NaHCO3

Perchloric acid is HClO4

Ammonium Oxide is (NH4)2O

You just need to master the multifarious groups and types of cations and anions.

You can use Quizlet.com to learn them