What to do: The best guide to transitional language is an appreciation of and respect for the needs of your audience. Don't ask yourself so much what you want to say as what your audience needs to know to be convinced of your claims. It also helps to have a good vocabulary of transitional words and phrases, so that you don't become dependent on a single device, such as therefore, to communicate what you mean. Writing from A to Z provides a good list of transitional words and phrases "classified according to function" (page 497), but keep in mind that two words can have the same function without being the same part of speech. For example, both but and although can be used to show contrast, but they don't have the same use in the grammar of sentences. Whereas although is a subordinating conjunction, but is a coordinating one.
The readability checklist that is part of the LARC Electronic Writing Center offers extended advice about transitional language, but there is one fairly common problem, connected with transition, that you can easily proofread for. Don't oversubordinate! You probably don't need both although and but in the same sentence.
NOT Although
Marlow is in awe of Kurtz, but he doesn't trust him.
EITHER Although
Marlow is in awe of Kurtz, he doesn't trust him.
OR Marlow
is in awe of Kurtz, but he doesn't trust him.