As for the first question, you can simply explicitly indicate the subject in your second relative clause.
Bangohan o tabenakatta bobu wa, watashi ga eiga de mita ginko ni itta.
As for the second question, how a relative clause modifies the following noun depends on what is said or unsaid in the relative clause. Let's start from this simple sentence:
Watashi wa eiga de ginko wo mita.
I saw a bank in the movie.
You can make three noun phrases from this:
eiga de ginko wo mita hito
the person who saw a bank in the movie
watashi ga eiga de mita mono
the thing which I saw in the movie
watashi ga ginko wo mita eiga
the movie where I saw a bank
As you can see, there is no word that corresponds to English relative pronouns (eg "which", "who", "where", "that") which can indicate the grammatical role of the relative clause. This means this phrase can be theoretically ambiguous:
- the movie where [I/he/etc] saw a bank
- the movie that saw a bank (?)
In most cases this is not a problem, because everyone knows a movie is an inanimate object can't see something. However, you can still make an ambiguous phrase which can be interpreted in two ways if there is no context:
hon o kashita hito
- the person who lent a book (to someone)
- the person whom [I/he/etc] lent a book
watashi ga suki na neko
- the cat who likes me
- the cat I like