Graphs from two sets of data files with different number of datapoints
Ok, addressing the points as best I can without an example of what you tried that didn't work...

How to import to sets of data and how to choose specific column in each of them (would it be exactly the same as if dealing with one file)?

You'd import each file separately. Assuming your file has headers, something like

d1 <- read.csv("your_file1_name.csv", headers=TRUE)
d2 <- read.csv("your_file2_name.csv", headers=TRUE)

If your headers name useful names (e.g. "Time", "88height", "number of octopus", etc), your data frame will have the same column names, after running the headers through make.names(), which coverts the titles to legal R data frame column names.
e.g.

d1$Time
d1$number.of.octopus
d2$X88height

If you want the data frames merged into one big data frame, use rbind().
If you want a vector of all the data from a particular column from each data frame, you'd use c()
e.g. 

total.octopus <- c(d1$number.of.octopus, d2$number.of.octopus)


One of the file have much more data points than the other (3 600 000 vs 80 000). How can I select every nth row in the csv file?

To select every 9th row of, say, d1, you'd index:

idx <- seq(1, nrow(d1), by=9)
d1_samp <- d1[idx,]  #note the comma and blank - means "every column"

Because of the lack of examples, this is only my interpretation of your needs. If it doesn't answer your question, you'll get there faster if you post a sample or toy example of code we can run that shows what you tried. For example, what kind of graph are you trying to make? Scatterplot? Trend? Barchart? And what kind of data? Time series? Number-vs-category? etc.
I want to produce a graph from two sets of data files (txt and csv) and I have encountered a couple of issues using either R or Python and would be super super grateful if somebody could help :)

How to import to sets of data and how to choose specific column in each of them (would it be exactly the same as if dealing with one file)? 
One of the file have much more data points than the other (3 600 000 vs 80 000). How can I select every nth row in the csv file? 

I would be grateful for any help in either R or python