"We will come to Dodoma"
'na' means 'and' or 'with'. The word 'kuja' means 'to come', and when it is followed by a place it means 'come to'. In some cases prepositions don't work the same in English and Swahili, especially when locative adverbs are involved e.g. 'anaishi Marekani' means 'she/he lives in America'
No, that would mean "We will come we are in Dodoma." It's like you're mixing the two sentences:
Tutakuja Dodoma. = We will come to Dodoma.
Tupo Dodoma. = We are in Dodoma.
(By the way, I think tuko would be more common with people in a city. A city is very big compared to a person, so the city is not really a precise location.)