Indirect questions can be tricky to form in Latin. Here's a guide to make sure you form it right every time. The best way to learn them is to learn the differences between direct and indirect questions.
Question words
In direct questions of the form, "is x the case or not?" then the "or not" at the end of the question is expressed by the word annon. In indirect questions (eg "he asked if the soldiers had won or not") you use necne instead.
All indirect factual questions (questions beginning "if" or "whether" eg "he asked whether the soldiers had won") use num, not si, to mean whether.
Instead of using cur to mean "why", indirect questions use quare or quam ob rem
Instead of using quomodo to mean "how", indirect questions use quem ad modum
Tense and mood
When you compose an indirect question, the best way to start is by thinking about what the original direct question would have been.
eg "He asked if the men had fled" --> "have the men fled?"
"She asked if the battle was being won" --> "is the battle being won?"
You can then use this table to change the verb in the original direct question so that it can be used in an indirect question.
Original present tenses become present subjunctive in primary sequence and imperfect subjunctive in historic sequence
Original future tenses in primary sequence use the future participle and present subjunctive of sum (or present subjunctive if there is no future participle), and in historic sequence use the future participle and imperfect subjunctive of sum, or just the imperfect subjunctive if there is no future participle
Original past tenses become perfect subjunctive in primary sequence and pluperfect subjunctive in historic sequence
Don't forget!
When se and suus are used in indirect questions, they refer to the subject of the main verb. In other instances when you need pronouns, use parts of is, ea, id.