Re. tenses - choice of tense is entirely up to you, but make sure you have considered the reason/s for your choice, and that they will make sense to your reader (e.g. does use of present tense make past events sound more immediate?).
Sometimes re-writing a paragraph in different tenses can help clarify which tense 'feels' most suitable.
If your reader can clearly understand when your action takes place, there should be no real issue with which tense you choose. However, if you want to make things less explicit (leave the reader to work out what is happening when) then you may need to reconsider your choice of tenses.
Re. telling a story with long flashbacks:
Try to make sure you have strong connections between flashback and present day, a logical reason to structure a past narrative at that point, and that the flashback is always necessary to your plot. Then structure it in a way that makes sense to you - it's your story.
I recommend asking others for feedback quite early on, to see what their impression is as readers of how both these issues are working in your story.