Sometimes I see tones written with numbers and other times with little tone marks. Is there any difference?
Good question.
Since Chinese has tones, we need to use tone markers when writing pinyin. There are two common ways to do this.
###With Diacritics:
These are the little symbols above the main vowel sound. They don’t take up much space, and don’t get in the way as much as numbers when reading long pinyin sentences. They are written thusly;
- 1st tone (ī, ā)
- 2nd tone (í, á)
- 3rd tone (ǐ, ǎ)
- 4th tone (ì, à)
- 5th neutral tone (no tone marker needed)
###With numbers:
ni3 hao3, wo3 shi4 mei3 guo2 ren2
This method is much quicker to type on a keyboard since it’s much easier to choose a number than long hold down on the keyboard to get a list of special characters*.
I also find it harder to read with numbers personally speaking.
###Comparison
Here are the two compared. You can decide which you prefer.
Nǐ hǎo, wǒ shì měiguó rén
ni3 hao3, wo3 shi4 mei3 guo2 ren2
###Further Reading
*I might be wrong, but I believe the number system came about because old typewriters didn’t have all the different symbols that modern computers have so it was easier to write with numbers. Numbers are also a great way to search for characters using dictionaries such as Pleco or MDBG since it narrows now the search options.
In order to get the diacritics on a Mac, just long hold on a vowel and you should get some options. You then pick the corresponding number. Note that I can’t find a 3rd tone diacritic which is super annoying. In this case I copy past from MDGB or Google Translate.
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As @gwilymjames points out there are two ways to note tones in chinese
with diacritics and with numbers.
With numbers you add the tone number after the pinyin, quite straightforward. 
hao3
Now with diacritics on which vowel do you put the diacritic ? hǎo ou haǒ one is correct the other wrong. 
There is a rule but very seldom described in textbooks.
If there are several vowels the diacritic is placed on the more important vowel.
The order of importance of vowels is given by the list a o e u i (from most important to less important). But if there are only u and i the diacritic is always placed on the last one (liù duì).
So hǎo is the correct transcription.
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