With some exceptions, that company generally uses its assets very effectively.
Literal
Exceptions exist but, that company [topic-は] usually assets [object-を] very well uses-ている.
The clause 例外もあるが ('exceptions exist, but') uses が as a conjunctive 'but.' たいていは ('mostly, usually') is adverbial with a contrastive は. とてもうまく modifies 利用している. A nuanced business statement using concessive+generalizing structure.