Dictionaries differ in definitions and presentation, and may cause confusion if not used correctly. A definition can only capture the interpretation of those who wrote it, and may not encompass all usable meanings or contexts. If you do not know another Asian language already, then how to express concepts and use words in Japanese will be much more different. It will take time to encounter and understand these differences. As such, dictionaries can only be used as a guide.
When consuming Japanese, there should be little problem using a bilingual dictionary that shows definitions in your native language. Even if a word is used differently between languages, the context of the word in the Japanese should allow you to interpret the correct meaning. Take for example the word 気分 - a Japanese-English dictionary may show results such as “feeling, mood”. However, it is likely problematic when searching from one’s native language for Japanese words, because the dictionary will not be able to take into account the context. Take for example the word “feeling” - a Japanese-English dictionary may show results such as “気分, 感じ, 気持ち”. Now there are three results, and it isn’t clear which to use. When communicating it is best to use only words you have encountered, especially when ambuguity exists.
Almost all free Japanese-English dictionary websites and applications share this problem, as they all use the same community created EDICT/JMDIC dictionary, including Jisho.org, Japanese Readifier, and YomiChan. A number of these websites and applications make it possible to keep track of encountered words and export word definitions which can be imported into flashcard applications like Anki. Despite being a community created dictionary that lacks oversight and polish found in commercial dictionaries, it serves its purpose for beginners and when complete understanding of words is not necessary. In fact, complete understanding is probably not necessary most of the time. However, the example sentences incorporated in these websites and applications are likely best avoided. And, for when deeper understanding is necessary, beginners can make use of the Cambridge Dictionary and Japanese Learner’s Dictionary.
On the other hand, the majority of Japanese monolingual dictionaries are created to a higher standard and display usage, differences, and nuance of words in near entirety, but are only searchable from licensed websites and paid applications. As these dictionaries are Japanese-only, they are most helpful once beyond the beginner stages. However, beginners can still make use of them by slowly translating results, or even using machine translation in an attempt to grasp the overall meaning. These dictionaries are searchable for free on websites such as Weblio, ALC, Goo and Kotobank. Goo and Kotobank both show whether a spelling variation is commonly used, where × shows not in use, ▽ shows not used much, and △ shows common usage. Goo also offers a dedicated lookup for distinguishing synonyms. Although Goo also has an English-only page, it has issues similar to that of EDICT.
Definitions of specialist and casual terminology may not be easily found in usual dictionaries. For example, e-words may be consulted for computing terms, and Zokugo, Pixiv and NicoVideo may be consulted for slang, such as from manga, anime, and informal conversation, similar to UrbanDictionary for English.
For further context or example sentences, try using a corpus - a database of searchable sentences - such as ALC, Weblio, Linguee, and Reverso. And when dictionaries and corpora aren’t enough, search or ask questions related to the problem at the Japanese StackExchange, LearnJapanese Reddit, or HiNative. There’s also Google Japan, where differences between words can be found by searching “WordAとWordBの違い”, and meanings or translations can be found by searching “phraseとは” or “日本語でphraseの意味”. The meaning of kanji in a word may also aid understanding, although this isn’t always the case.
Know Your Goals
Looking up every new word encountered could be quite tedious. Especially if using a monolingual dictionary, and if there are also unknown words in those definitions, and if looking up those unknown words as well. Regardless of using a monolingual or bilingual dictionary, it could also be tedious to learn every usage or meaning that a word carries. Dictionaries tend to be verbose and informative, and are not necessarily practical. It cannot be expected one will internalize the usage and feeling of a word by dictionary alone. Such learning styles could lead to a downward spiral of distraction from study, causing a loss of enjoyment in the language as it becomes a chore.
Instead, it may be more sane to only look up words seen more than once in a text, or when it seems to be the key word in a sentence. If a word is important, it’ll come up again later at some point. A bilingual dictionary should be sufficient for most word lookups, and ease one’s transition into language acquisition, and take up much less effort and time. In fact, this may become a long-term method of study even if monolingual definitions can be understood. Then, a monolingual dictionary could be reserved only for when there is confusion and differences between terms that need to be understood. If exporting definitions into flashcard applications, then modify those definitions to focus on practical use, such as by making parts of the definition bold or including example sentences. And, flashcard applications should only be used to review newly encountered information, not to learn new information where context is scarce and information is isolated.
This is a balancing act of time, efficiency, enjoyment, and practicality for your goals.
Tools to Learn Efficiently
Japanese Readifier makes it possible to grade the difficulty of texts, look up definitions, and export definitions quickly.
MultiSiteSearcher makes it possible to search multiple dictionary and corpus websites at the same time.
Japanese Text Analaysis and Readability Tools is a post about various other tools.