the question is on the tin, i am new to 6mm painting and was looking at getting one of the roman legion boxes, but see that it does not come with bases, what scale of bases should i use for each unit?

specifically, the hail ceasar early imperial rome army pack. also, do the models come with instructions on how to base them?

It does depend upon what rules you are using, your level of abstraction and what you are trying to represent in terms of size of battle/armies and how much detail you want to go into.

My Roman legions are based on cohorts with each cohort being 8 figures and on a 25x12mm base. But then I'm fairly unique.....

The other point to consider is who the Romans will be fighting and how will they be based? It it probably important that both sides operate on a similar scale and basing regime to reflect history (even to a limited degree).

If you look at the gallery section, you'll see different representations and basing regimes.

With Hail Caesar, the rules themselves are pretty flexible on this point. The only broad recommendation is that a standard-sized unit should cover 12-16cm. The key issue is how flexible you want each unit to be in terms of the formations allowed. Hail Caesar has 'battle lines' (close order), 'column', 'open order', 'square', 'testudo', 'warband'. So if you want each unit to be flexible enough to show all this, then you will probably prefer a number of smaller bases in order to show this visually. If you don't care, or are happy to mark a unit with a command figure to denote its formation, then you can have the entire unit on a single base. 
Given a close-order unit in the Hail Caesar army pack is 48 models, I imagine that they had in mind either 3-4 x 40x20mm bases/unit, with 2 ranks of 6-8 figures on each; or 2 x 60x30mm bases/unit, with either 2 ranks of 12 figures or 3 ranks of 8 figures on each of them. 

I believe Hail Caesar in 28mm is played on 40x40mm bases. I have seen online some that use the same base size with 6mm figures. 

If I were to go with Hail Caesar (or Age of Hannibal) I would go for 40x40mm bases with up to four rows of close ordered infantry. The Baccus pack has, if you go for 40x40mm bases, enough figures for 6 row per base (48 figures). 

I think it's important to ask yourself against who you will be playing. Are you going to join a club? Then it might be easier to base them up the same as the majority at the club does. If you are going to solo, then go wild.